Pierrick Roger
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:33 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2025-04-01 12:11:49 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 12:13:21 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 92.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-04-01 12:12:44.153][biodb::testContext]
biodb.INFO [2025-04-01 12:12:44.159][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:12:44.160][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-01 12:12:44.161][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:12:44.163][biodb::testContext]
biodb.INFO [2025-04-01 12:12:44.171][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:12:44.173][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 12:12:44.183][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:12:44.184][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 12:12:44.185][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.189][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 12:12:44.233][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.236][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.DEBUG[2025-04-01 12:12:44.237][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 12:12:44.238][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.241][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 12:12:44.242][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 12:12:44.243][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 12:12:44.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.246][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 12:12:44.247][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 12:12:44.248][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.252][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 12:12:44.255][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 12:12:44.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.261][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 12:12:44.262][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 12:12:44.264][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 12:12:44.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.267][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 12:12:44.268][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.271][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 12:12:44.272][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 12:12:44.273][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 12:12:44.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.276][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:12:44.277][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 12:12:44.278][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 12:12:44.278][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 12:12:44.279][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 12:12:44.280][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 12:12:44.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.282][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[2025-04-01 12:12:44.283][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 12:12:44.284][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 12:12:44.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.287][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 12:12:44.288][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 12:12:44.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.291][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 12:12:44.295][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 12:12:44.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.299][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 12:12:44.301][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 12:12:44.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.305][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 12:12:44.306][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 12:12:44.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.313][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:12:44.315][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 12:12:44.347][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 12:12:44.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.354][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 12:12:44.356][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 12:12:44.357][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 12:12:44.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.364][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 12:12:44.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.434][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 12:12:44.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.436][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:12:44.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.440][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.443][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.445][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:12:44.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:12:44.447][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.448][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 12:12:44.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:12:44.450][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.451][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.452][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:12:44.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:12:44.452][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:12:44.452][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:12:44.452][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:12:44.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:12:44.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.456][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:12:44.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.466][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.467][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:12:44.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:12:44.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.470][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.471][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 12:12:44.473][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.474][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:12:44.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:12:44.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.479][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:12:44.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:12:44.481][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.482][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 12:12:44.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:12:44.484][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:12:44.485][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:12:44.486][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:12:44.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:12:44.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.494][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:12:44.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:12:44.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.498][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.499][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 12:12:44.501][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.502][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 12:12:44.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:12:44.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.506][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.507][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:12:44.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:12:44.509][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.510][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 12:12:44.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:12:44.511][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.513][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:12:44.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:12:44.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.520][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:12:44.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:12:44.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.523][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.524][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 12:12:44.526][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.527][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:12:44.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.528][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:12:44.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.531][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.532][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.533][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:12:44.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:12:44.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.535][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 12:12:44.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:12:44.537][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.538][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.540][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:12:44.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:12:44.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.551][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:12:44.553][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:12:44.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.554][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:12:44.559][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:12:44.560][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.599][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[2025-04-01 12:12:44.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.619][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[2025-04-01 12:12:44.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.623][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[2025-04-01 12:12:44.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.647][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 12:12:44.653][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 12:12:44.654][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 12:12:44.656][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 12:12:44.657][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:12:44.658][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 12:12:44.659][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 12:12:44.661][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 12:12:44.662][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 12:12:44.663][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 12:12:44.664][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:12:44.666][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 12:12:44.667][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 12:12:44.668][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 12:12:44.669][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 12:12:44.671][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 12:12:44.673][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 12:12:44.675][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 12:12:44.678][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:12:44.680][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 12:12:44.682][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 12:12:44.683][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 12:12:44.684][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 12:12:44.686][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 12:12:44.687][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 12:12:44.688][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 12:12:44.689][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 12:12:44.691][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 12:12:44.692][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 12:12:44.693][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 12:12:44.694][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 12:12:44.695][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 12:12:44.697][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 12:12:44.702][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 12:12:44.705][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 12:12:44.709][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 12:12:44.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 12:12:44.713][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 12:12:44.715][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 12:12:44.716][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 12:12:44.717][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 12:12:44.719][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 12:12:44.720][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 12:12:44.721][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 12:12:44.722][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 12:12:44.723][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 12:12:44.725][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 12:12:44.726][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 12:12:44.727][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 12:12:44.728][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 12:12:44.729][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 12:12:44.730][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 12:12:44.732][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 12:12:44.733][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 12:12:44.734][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 12:12:44.735][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 12:12:44.736][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 12:12:44.737][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 12:12:44.739][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 12:12:44.740][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 12:12:44.744][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 12:12:44.746][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 12:12:44.749][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 12:12:44.751][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 12:12:44.753][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 12:12:44.755][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 12:12:44.756][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:12:44.758][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:12:44.760][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 12:12:44.761][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 12:12:44.762][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 12:12:44.764][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 12:12:44.765][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 12:12:44.766][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 12:12:44.767][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 12:12:44.768][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 12:12:44.770][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 12:12:44.771][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 12:12:44.772][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 12:12:44.773][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 12:12:44.774][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 12:12:44.775][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 12:12:44.777][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 12:12:44.784][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 12:12:44.787][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:12:44.791][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:12:44.792][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.794][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.811][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[2025-04-01 12:12:44.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.837][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[2025-04-01 12:12:44.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.856][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[2025-04-01 12:12:44.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.861][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[2025-04-01 12:12:44.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.867][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[2025-04-01 12:12:44.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.896][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[2025-04-01 12:12:44.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.901][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[2025-04-01 12:12:44.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.906][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[2025-04-01 12:12:44.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.912][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[2025-04-01 12:12:44.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:12:44.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:44.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:44.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:44.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:44.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:44.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:44.924][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 12:12:44.934][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 12:12:44.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.939][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:12:44.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.946][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.947][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 12:12:44.948][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 12:12:44.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:12:44.949][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.950][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 12:12:44.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 12:12:44.952][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 12:12:44.953][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 12:12:44.954][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:12:44.954][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:12:44.954][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:12:44.955][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 12:12:44.956][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:12:44.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:12:44.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:12:44.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:12:44.960][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:44.960][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 12:12:44.961][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:12:44.962][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:12:44.963][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 12:12:44.964][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 12:12:44.964][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 12:12:44.973][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:12:44.977][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:12:44.979][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 12:12:44.981][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:12:44.983][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:12:44.985][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:12:45.017][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 12:12:45.019][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 12:12:45.025][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 12:12:45.031][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 12:12:45.037][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:12:45.038][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:12:45.040][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 12:12:45.041][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 12:12:45.053][biodb::testThat]
biodb.INFO [2025-04-01 12:12:45.054][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-04-01 12:12:45.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:45.056][biodb::testThat]
biodb.TRACE[2025-04-01 12:12:45.061][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-04-01 12:12:45.076][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:45.080][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:45.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:45.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:45.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:45.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:45.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:45.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:45.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:45.130][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.153][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.154][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.196][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.198][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.200][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.205][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:45.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:45.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.208][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.212][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.219][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.220][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.222][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.223][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.226][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:45.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.234][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:45.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.241][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.243][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.248][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:45.312][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.317][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:45.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.326][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.330][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.332][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:45.417][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-01 12:12:45.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:45.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:45.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:45.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:45.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:45.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:45.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:45.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:45.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:45.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.497][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:45.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:45.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.649][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.654][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:45.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.692][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.695][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:45.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.730][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.732][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:45.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.770][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.771][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.773][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:45.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:45.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.798][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.804][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:45.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.836][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:45.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.864][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.870][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.871][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.875][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.876][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:45.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:45.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.901][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.905][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.907][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:45.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.930][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.934][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.937][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.941][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:45.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.953][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.965][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.966][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.971][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:45.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:45.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:45.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:45.998][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.999][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:45.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.000][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.043][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.044][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.070][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.073][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.079][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:46.080][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:46.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.083][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.089][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:46.091][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:46.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.093][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.098][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.099][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.112][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.121][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.123][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.125][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.133][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:46.134][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:46.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.136][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.145][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.147][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.156][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 12:12:46.158][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:46.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.169][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.177][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:46.179][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:46.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.180][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 12:12:46.196][biodb::testThat]
biodb.INFO [2025-04-01 12:12:46.197][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-01 12:12:46.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:46.202][biodb::testThat]
biodb.DEBUG[2025-04-01 12:12:46.219][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-01 12:12:46.228][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:46.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-01 12:12:46.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:46.236][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-01 12:12:46.237][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:46.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:46.274][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:46.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:46.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:46.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:46.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:46.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:46.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:46.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:46.292][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.321][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:46.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:46.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.324][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:46.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:46.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.329][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:46.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:46.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.332][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:46.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:46.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.342][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:46.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.346][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.347][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.349][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:46.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.354][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.355][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.356][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:46.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.361][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:46.362][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:46.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.363][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.365][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:46.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:46.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.371][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.374][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.377][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:46.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.382][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.383][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.392][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.418][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:46.421][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:46.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.424][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.426][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:46.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:46.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.429][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:46.430][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:46.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.432][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:46.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:46.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:46.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:46.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:46.474][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-01 12:12:46.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-01 12:12:46.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-01 12:12:46.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-01 12:12:46.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-01 12:12:46.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-01 12:12:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-01 12:12:46.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:12:46.501][biodb::testThat]
biodb.INFO [2025-04-01 12:12:46.503][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-01 12:12:46.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:46.504][biodb::testThat]
biodb.TRACE[2025-04-01 12:12:46.508][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.509][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.510][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:46.512][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-01 12:12:46.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:46.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:46.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:46.572][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-01 12:12:46.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 12:12:46.603][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:12:46.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 12:12:46.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:46.624][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 12:12:46.659][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:46.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:46.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:46.666][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:12:47.045][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:12:47.280][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:47.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-01 12:12:47.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-01 12:12:47.308][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-01 12:12:47.331][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:47.333][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:47.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.335][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.336][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.337][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.350][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 12:12:47.357][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.358][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-04-01 12:12:47.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:47.360][biodb::testThat]
biodb.TRACE[2025-04-01 12:12:47.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:47.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:47.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:47.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:47.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:47.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:47.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:47.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:47.484][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:12:47.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:12:47.488][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:47.490][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-01 12:12:47.512][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.513][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-04-01 12:12:47.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:47.515][biodb::testThat]
biodb.TRACE[2025-04-01 12:12:47.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:47.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:47.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:47.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:47.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.568][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:47.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:47.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:47.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:47.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:47.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:47.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:47.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:47.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:47.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.645][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 12:12:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:47.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 12:12:47.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:47.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 12:12:47.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:47.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:12:47.673][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.674][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-01 12:12:47.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:47.676][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.688][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.691][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-01 12:12:47.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:47.693][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.703][biodb::testThat]
biodb.INFO [2025-04-01 12:12:47.704][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-01 12:12:47.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:47.706][biodb::testThat]
biodb.DEBUG[2025-04-01 12:12:47.711][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-01 12:12:48.020][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-01 12:12:48.387][biodb::testThat]
biodb.INFO [2025-04-01 12:12:48.400][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-01 12:12:48.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:48.402][biodb::testThat]
biodb.DEBUG[2025-04-01 12:12:48.519][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-04-01 12:12:48.640][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:48.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:48.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.644][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.645][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:48.646][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:48.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.648][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 12:12:48.650][biodb::testThat]
biodb.INFO [2025-04-01 12:12:48.651][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-04-01 12:12:48.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:12:48.653][biodb::testThat]
biodb.TRACE[2025-04-01 12:12:48.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:48.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:48.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:48.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:48.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:48.790][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:12:48.791][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:12:48.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:48.797][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 12:12:48.891][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:48.894][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:12:48.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:12:48.897][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:48.899][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-01 12:12:48.921][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 12:12:48.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 12:12:48.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:48.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:48.972][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:48.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:48.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:49.015][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:12:49.119][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:12:49.217][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:49.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-01 12:12:49.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-01 12:12:49.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:49.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:49.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:49.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:49.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:49.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:49.243][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.DEBUG[2025-04-01 12:12:49.244][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-01 12:12:49.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:49.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-01 12:12:49.310][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:49.311][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:49.313][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:49.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:49.317][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:49.318][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:49.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:49.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:49.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:49.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:49.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:49.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:49.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:49.342][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-01 12:12:49.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:49.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:49.347][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-01 12:12:49.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-01 12:12:49.554][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:49.557][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-01 12:12:49.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-01 12:12:49.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-01 12:12:49.569][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:49.570][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:49.571][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:49.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:49.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:49.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:49.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:49.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:49.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:49.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:49.593][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.595][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.598][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.603][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:49.604][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:49.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.606][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.645][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:49.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.650][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:49.651][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:49.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.652][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:49.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.658][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:49.660][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:49.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.661][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:49.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:49.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.666][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:49.667][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:49.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.669][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:49.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:49.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.673][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:49.674][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:49.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.676][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.677][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:49.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:49.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.693][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:49.694][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:49.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.696][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.701][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:49.702][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:49.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.703][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:49.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:49.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.708][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:49.709][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:49.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.711][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.712][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:49.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:49.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.715][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:49.716][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:49.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.718][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:49.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:49.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:49.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:49.819][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-01 12:12:49.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:49.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:49.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:49.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:49.843][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:49.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:49.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:49.871][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:12:49.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:12:50.088][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:50.094][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-01 12:12:50.100][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-01 12:12:50.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:50.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:50.161][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-01 12:12:50.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:50.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-01 12:12:50.171][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:50.173][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:50.174][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:50.175][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:50.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:50.178][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:50.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:50.227][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-01 12:12:50.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:50.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:50.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-01 12:12:50.333][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-01 12:12:50.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:50.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-01 12:12:50.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-01 12:12:50.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-01 12:12:50.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:50.445][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:50.446][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:50.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:50.468][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.471][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.476][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:50.477][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:50.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.479][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.508][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.514][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:50.515][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:50.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.517][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:50.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:50.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:50.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:50.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:50.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:50.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.554][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:50.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:50.561][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:50.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.565][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.567][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:50.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.570][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.571][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:50.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.576][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:50.578][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:50.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.580][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:50.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.588][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:50.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:50.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.593][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:50.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:50.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.599][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:50.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:50.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.602][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.603][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:50.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:50.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.612][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:50.614][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:50.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.615][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.617][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:50.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:50.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:50.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:50.668][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-01 12:12:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:50.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:12:50.731][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:12:50.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:12:50.733][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:12:50.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 12:12:50.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:50.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:50.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:50.787][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-01 12:12:50.788][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:50.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-01 12:12:50.791][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:50.793][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:50.794][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:50.795][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:50.796][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:50.798][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:50.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:50.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:50.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:50.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:50.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:50.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:50.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:50.812][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-01 12:12:50.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:50.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:50.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-01 12:12:50.910][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-01 12:12:51.012][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:51.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-01 12:12:51.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-01 12:12:51.024][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-01 12:12:51.026][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:51.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:51.029][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:51.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:51.045][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.054][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:51.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:51.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.057][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.058][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:51.059][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:51.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.062][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:51.063][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:51.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.065][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.068][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:51.069][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:51.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:51.087][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:51.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.089][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.091][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:51.091][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.093][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:51.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:51.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.097][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.098][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:51.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:51.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.103][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:51.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:51.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.136][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:51.137][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:51.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.140][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:51.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:51.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:51.145][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:51.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.146][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:51.192][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-01 12:12:51.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:51.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:51.229][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-01 12:12:51.230][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:51.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-01 12:12:51.233][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:51.234][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:51.235][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:51.236][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:51.238][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:51.239][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:51.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:51.253][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-01 12:12:51.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:51.283][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:51.284][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-01 12:12:51.383][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-01 12:12:51.600][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:51.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-01 12:12:51.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-01 12:12:51.609][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-01 12:12:51.611][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:51.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:51.613][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:51.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.625][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[2025-04-01 12:12:51.627][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.631][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.638][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:51.639][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:51.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.641][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.642][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:51.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:51.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.646][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.647][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:51.649][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:51.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.650][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.651][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:51.652][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:51.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.654][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.655][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:51.656][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:51.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.658][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.659][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:51.660][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.662][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.663][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:51.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:51.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.665][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.666][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:51.667][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:51.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.669][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:51.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:51.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.712][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:51.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:51.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.716][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:51.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:51.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.720][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:51.721][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:51.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.723][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:51.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:51.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:51.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:51.772][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-01 12:12:51.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:51.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:51.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:51.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:51.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:51.815][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-01 12:12:51.816][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:51.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-01 12:12:51.819][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:51.820][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:51.822][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:51.823][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:51.824][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:51.825][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:51.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:51.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:51.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:51.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:51.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:51.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:51.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:51.842][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-01 12:12:51.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:51.870][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:51.872][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-01 12:12:51.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-01 12:12:52.050][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:52.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-01 12:12:52.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-01 12:12:52.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-01 12:12:52.064][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:52.066][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:52.067][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:52.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:52.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:52.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:52.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:52.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:52.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:52.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:52.098][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.109][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:52.110][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:52.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.112][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.113][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:52.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:52.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.118][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:52.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:52.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.123][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.124][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.127][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.132][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.134][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:52.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.141][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.142][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.144][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.145][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:52.146][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:52.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.148][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:52.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.181][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:52.184][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:52.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.187][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.188][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:52.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:52.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.201][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:52.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:52.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.203][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:52.244][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-01 12:12:52.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:52.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:52.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:52.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:52.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:52.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:52.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:52.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:52.284][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-01 12:12:52.285][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:52.287][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-01 12:12:52.288][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:52.289][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:52.291][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:52.294][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:52.296][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:52.297][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:52.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:52.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:52.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:52.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:52.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:52.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:52.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:52.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-01 12:12:52.349][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:52.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:52.352][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-01 12:12:52.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-01 12:12:52.574][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:52.576][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-01 12:12:52.581][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-01 12:12:52.584][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-01 12:12:52.586][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:52.588][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:52.589][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:52.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:52.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:52.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:52.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:52.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:52.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:52.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:52.604][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.605][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.607][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.612][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:52.613][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:52.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.615][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:52.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:52.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.665][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:52.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:52.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.669][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.674][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:52.675][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:52.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.676][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:52.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:52.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.681][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.682][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.688][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.692][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.693][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:52.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.697][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:52.698][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.700][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.705][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.710][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:52.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.716][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:52.717][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:52.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.719][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:52.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.725][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:52.726][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:52.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.727][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.729][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:52.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:52.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.979][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:52.980][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:52.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:52.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:52.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:52.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:52.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:52.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:52.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:53.031][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-01 12:12:53.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:53.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:53.061][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-01 12:12:53.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:53.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-01 12:12:53.064][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:53.065][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:53.066][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:53.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:53.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:53.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:53.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:53.082][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-01 12:12:53.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:53.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:53.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-01 12:12:53.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-01 12:12:53.314][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:53.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-01 12:12:53.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-01 12:12:53.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-01 12:12:53.329][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:53.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:53.332][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:53.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.348][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.TRACE[2025-04-01 12:12:53.351][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.352][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.356][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.363][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:53.364][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:53.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.366][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:53.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:53.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.403][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:53.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:53.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.406][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.412][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:53.413][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:53.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.416][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:53.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:53.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.421][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.422][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.424][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.429][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.430][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.432][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.433][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.437][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:53.438][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.440][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.442][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:53.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.447][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.458][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:53.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:53.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:53.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.468][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:53.469][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:53.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.470][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.472][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:53.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:53.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.476][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:53.477][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:53.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.479][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:53.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:53.521][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-01 12:12:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:53.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:53.555][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-01 12:12:53.556][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:53.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-01 12:12:53.560][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:53.561][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:53.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:53.563][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:53.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:53.565][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:53.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:53.593][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-01 12:12:53.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:53.616][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:53.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-01 12:12:53.717][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-01 12:12:53.812][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:53.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-01 12:12:53.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-01 12:12:53.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-01 12:12:53.823][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:53.824][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:53.825][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:53.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:53.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:53.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:53.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:53.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:53.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:53.842][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.TRACE[2025-04-01 12:12:53.845][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.846][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.847][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.855][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:53.856][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:53.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.892][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:53.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:53.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.894][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:53.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:53.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.899][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:53.900][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:53.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.902][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.906][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.907][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.908][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:53.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.913][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.914][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:53.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.915][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.916][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:53.917][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.922][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.924][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:53.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:53.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.930][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.931][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.933][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.938][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:53.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:53.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:53.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.947][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:53.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:53.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:53.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:53.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.957][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:53.958][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:53.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:53.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:53.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:53.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:53.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:53.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:53.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:53.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:53.999][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-01 12:12:54.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:54.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:54.027][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-01 12:12:54.028][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:54.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-01 12:12:54.031][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:54.033][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:54.035][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:54.036][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:54.037][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:54.038][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:54.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:54.053][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-01 12:12:54.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:54.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:54.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-01 12:12:54.202][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-01 12:12:54.292][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:54.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-01 12:12:54.301][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-01 12:12:54.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-01 12:12:54.307][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:54.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:54.310][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:54.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:54.328][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.329][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.331][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.336][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:54.337][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:54.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.338][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.379][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:54.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:54.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.383][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:54.384][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:54.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.386][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.388][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:54.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:54.394][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:54.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.396][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:54.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:54.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.401][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.402][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:54.412][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:54.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.415][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.416][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:54.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.422][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:54.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.437][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:54.438][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:54.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.440][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:54.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.449][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:54.450][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:54.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.452][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.458][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:54.460][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:54.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.463][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:54.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:54.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:54.508][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-01 12:12:54.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:54.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:54.539][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-01 12:12:54.539][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:54.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-01 12:12:54.542][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:54.543][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:54.544][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:54.545][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:54.547][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:54.548][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:54.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:54.564][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-01 12:12:54.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:54.586][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:54.588][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-01 12:12:54.695][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-01 12:12:54.800][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:54.803][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-01 12:12:54.807][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-01 12:12:54.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-01 12:12:54.811][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:54.813][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:54.814][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:54.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:54.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:54.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:54.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:54.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:54.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:54.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:54.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.831][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.836][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:54.837][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:54.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.838][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.877][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:54.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:54.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.882][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.884][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:54.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:54.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.890][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:54.891][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:54.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.893][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:54.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:54.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.898][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.899][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.900][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.906][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:54.907][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:54.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.909][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.910][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:54.911][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.913][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:54.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.921][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.922][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.931][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:54.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:54.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:54.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.940][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:54.940][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:54.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.943][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:54.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.946][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:54.947][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:54.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.949][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:54.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.006][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-01 12:12:55.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:55.031][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-01 12:12:55.032][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:55.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-01 12:12:55.035][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:55.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:55.037][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:55.038][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:55.039][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:55.040][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:55.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:55.061][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-01 12:12:55.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:55.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:55.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-01 12:12:55.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-01 12:12:55.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:55.279][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-01 12:12:55.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-01 12:12:55.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-01 12:12:55.287][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:55.288][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:55.290][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:55.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:55.311][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.314][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.321][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:55.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:55.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.323][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.355][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:55.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:55.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.359][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:55.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:55.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.362][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.367][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:55.367][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:55.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.369][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:55.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:55.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.374][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.374][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.376][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.381][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:55.382][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:55.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.383][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.385][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:55.385][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.387][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.392][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.393][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.395][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.400][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:55.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:55.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:55.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:55.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.407][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:55.408][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:55.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.410][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.411][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:55.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:55.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.415][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:55.416][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:55.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.418][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.471][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-01 12:12:55.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:55.508][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-01 12:12:55.509][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:55.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-01 12:12:55.512][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:55.513][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:55.514][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:55.515][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:55.516][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:55.516][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:55.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:55.537][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-01 12:12:55.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:55.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:55.574][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-01 12:12:55.674][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-01 12:12:55.773][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:55.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-01 12:12:55.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-01 12:12:55.784][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-01 12:12:55.787][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:55.790][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:55.792][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:55.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:55.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:55.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:55.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:55.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:55.812][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.821][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:55.822][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:55.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.824][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.861][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:55.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:55.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.865][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:55.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:55.875][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:55.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.877][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:55.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:55.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.884][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.885][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.888][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:55.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.896][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:55.896][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:55.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.898][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.899][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:55.900][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.902][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.904][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.910][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.911][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:55.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.917][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:55.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:55.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.920][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:55.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.925][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:55.926][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:55.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.930][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.931][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:55.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:55.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.935][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:55.936][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:55.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.938][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:55.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:55.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:55.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:55.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.983][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-01 12:12:55.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:55.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:55.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:55.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:55.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:55.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:55.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.005][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-01 12:12:56.005][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:56.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-01 12:12:56.008][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:56.009][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:56.010][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:56.011][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:56.012][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:56.012][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:56.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.032][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-01 12:12:56.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:56.056][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:56.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-01 12:12:56.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-01 12:12:56.240][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:56.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-01 12:12:56.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-01 12:12:56.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-01 12:12:56.252][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:56.253][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:56.255][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:56.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:56.271][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.273][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.281][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:56.281][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:56.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.283][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.314][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.319][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:56.320][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:56.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:56.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:56.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:56.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:56.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.342][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.344][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:56.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:56.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.347][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.348][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:56.349][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:56.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.351][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.352][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:56.353][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.357][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:56.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.361][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.362][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.364][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.368][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:56.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:56.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.371][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.378][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:56.379][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:56.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.380][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.382][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:56.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:56.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:56.386][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:56.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.387][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:56.421][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-01 12:12:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:56.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.453][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-01 12:12:56.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:56.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-01 12:12:56.457][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:56.459][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:56.461][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:56.462][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:56.464][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:56.465][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:56.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.482][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-01 12:12:56.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:56.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:56.505][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-01 12:12:56.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-01 12:12:56.696][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:56.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-01 12:12:56.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-01 12:12:56.707][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-01 12:12:56.710][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:56.712][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:56.713][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:56.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.725][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.TRACE[2025-04-01 12:12:56.728][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.729][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.730][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.735][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:56.736][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:56.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.738][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:56.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:56.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.772][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:56.773][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:56.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.774][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:56.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:56.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:56.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:56.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.784][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:56.787][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:56.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.789][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.790][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:56.791][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:56.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.793][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.794][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:56.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.797][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.803][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.804][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:56.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.812][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:56.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:56.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:56.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:56.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.820][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:56.821][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:56.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.823][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.824][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:56.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:56.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:56.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:56.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.831][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:56.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:56.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:56.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:56.879][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-01 12:12:56.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:56.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:56.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:56.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:56.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.915][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-01 12:12:56.916][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:56.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-01 12:12:56.918][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:56.920][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:56.924][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:56.926][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:56.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:56.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:56.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:56.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:56.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:56.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:56.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:56.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:56.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:56.965][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-04-01 12:12:56.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:56.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:56.989][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-04-01 12:12:57.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-04-01 12:12:57.178][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:57.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-04-01 12:12:57.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-04-01 12:12:57.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-04-01 12:12:57.191][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:57.193][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:57.194][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:57.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:57.214][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.215][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.217][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.221][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:57.223][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:57.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.257][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:57.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:57.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.263][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:57.264][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:57.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.266][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.268][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:57.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:57.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.272][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:57.273][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:57.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.274][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:57.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:57.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.282][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.283][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.285][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.291][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:57.293][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:57.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.296][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:57.297][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.298][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.299][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:57.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.303][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.304][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.305][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.310][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:57.311][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:57.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.313][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:57.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:57.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.318][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:57.318][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:57.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.320][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.323][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:57.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:57.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.329][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:57.330][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:57.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.332][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.333][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:57.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:57.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:57.375][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-01 12:12:57.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:57.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:57.397][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-01 12:12:57.398][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:57.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-01 12:12:57.401][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:57.402][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:57.403][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:57.404][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:57.406][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:57.407][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:57.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:57.425][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-04-01 12:12:57.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:57.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:57.449][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-04-01 12:12:57.552][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-04-01 12:12:57.648][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:57.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-04-01 12:12:57.656][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-04-01 12:12:57.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-04-01 12:12:57.661][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:57.663][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:57.664][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:57.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:57.691][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.694][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.700][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:57.701][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:57.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.703][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.732][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:57.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:57.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.737][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:57.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:57.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.740][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:57.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:57.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:57.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:57.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.749][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:57.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:57.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.756][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:57.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.763][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:57.764][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:57.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.769][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:57.770][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.773][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:57.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.777][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.778][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.780][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:57.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.785][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:57.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:57.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.788][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:57.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:57.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.796][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:57.797][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:57.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.799][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.800][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:57.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:57.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.804][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:57.805][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:57.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.806][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:57.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:57.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:57.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:57.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:57.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:57.849][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-01 12:12:57.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:57.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:57.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:57.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:57.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:57.871][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-01 12:12:57.871][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:57.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-01 12:12:57.874][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:57.875][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:57.876][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:57.877][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:57.878][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:57.878][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:57.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:57.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:57.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:57.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:57.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:57.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:57.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:57.893][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-04-01 12:12:57.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:57.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:57.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-04-01 12:12:58.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-04-01 12:12:58.115][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:58.118][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-04-01 12:12:58.126][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-04-01 12:12:58.129][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-04-01 12:12:58.131][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:58.135][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:58.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:58.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:58.154][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.155][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.157][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.162][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:58.163][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:58.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.165][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:58.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.200][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:58.201][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:58.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.202][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:58.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:58.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.208][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:58.210][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:58.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:58.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.219][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.220][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.222][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.228][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:58.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:58.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.231][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.233][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:58.235][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.237][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:58.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.264][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:58.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:58.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.266][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:58.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:58.273][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:58.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.276][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:58.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.279][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:58.280][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:58.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:58.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:58.318][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-01 12:12:58.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:58.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:58.341][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-01 12:12:58.342][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:58.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-01 12:12:58.345][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:58.346][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:58.347][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:58.348][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:58.349][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:58.351][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:58.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:58.370][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-04-01 12:12:58.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:58.398][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:58.400][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-04-01 12:12:58.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-04-01 12:12:58.610][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:58.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-04-01 12:12:58.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-04-01 12:12:58.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-04-01 12:12:58.624][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:58.626][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:58.627][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:58.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.647][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.TRACE[2025-04-01 12:12:58.650][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.653][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.662][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:58.662][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:58.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.664][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:58.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:58.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.702][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:58.703][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:58.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.706][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:58.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:58.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:58.716][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:58.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.718][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:58.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.723][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.724][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.730][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:58.731][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:58.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.732][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.735][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:58.737][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.740][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.741][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:58.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.745][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.746][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.750][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.757][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:58.757][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:58.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.760][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:58.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:58.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.767][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:58.768][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:58.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.770][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:58.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.775][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:58.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:58.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.778][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:58.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:58.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:58.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:58.827][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-01 12:12:58.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:58.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:58.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:58.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:58.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:58.868][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-01 12:12:58.869][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:58.870][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-01 12:12:58.871][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:58.872][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:58.873][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:58.874][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:58.875][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:58.876][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:58.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:58.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:58.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:58.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:58.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:58.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:58.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:58.891][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-04-01 12:12:58.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:58.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:58.917][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-04-01 12:12:59.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-04-01 12:12:59.115][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:59.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-04-01 12:12:59.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-04-01 12:12:59.124][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-04-01 12:12:59.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:59.127][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:59.128][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:59.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:59.144][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.156][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:59.157][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:59.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.187][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:59.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:59.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.191][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:59.193][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:59.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:59.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:59.201][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:59.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.204][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:59.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:59.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.210][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.211][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.213][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.218][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:59.218][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:59.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.222][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:59.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.239][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:59.240][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:59.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.242][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:59.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.249][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:59.250][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:59.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.252][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.253][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:59.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:59.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.257][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:59.258][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:59.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.260][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:59.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:59.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:59.310][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-01 12:12:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:59.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:59.342][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-01 12:12:59.343][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:59.345][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-01 12:12:59.347][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:59.348][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:59.349][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:59.350][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:59.351][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:59.352][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:59.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:59.369][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-04-01 12:12:59.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:59.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:59.393][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-04-01 12:12:59.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-04-01 12:12:59.580][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:12:59.584][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-04-01 12:12:59.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-04-01 12:12:59.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-04-01 12:12:59.597][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:12:59.599][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:12:59.600][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:12:59.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:12:59.620][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.621][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.623][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.628][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:59.629][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:59.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.631][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:12:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:12:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.678][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:59.679][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:59.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.681][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.683][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:12:59.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:12:59.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.688][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:59.690][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:59.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.692][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:12:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:12:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.699][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.700][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.701][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:12:59.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.706][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:59.707][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:12:59.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.708][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.709][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:59.710][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.712][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:12:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.716][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.717][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.719][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:12:59.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.723][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:59.724][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:59.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:12:59.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:12:59.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.731][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:59.732][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:59.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.733][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:12:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:12:59.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.738][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:59.739][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:59.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.741][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.742][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:12:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:12:59.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:12:59.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:12:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:12:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:59.780][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-01 12:12:59.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:12:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:12:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:12:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:12:59.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:59.803][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-01 12:12:59.804][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:12:59.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-01 12:12:59.808][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:12:59.808][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:12:59.809][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:12:59.810][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:12:59.811][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:12:59.812][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:12:59.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:12:59.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:12:59.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:12:59.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:12:59.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:12:59.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:12:59.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:12:59.828][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-04-01 12:12:59.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:12:59.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:12:59.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-04-01 12:12:59.958][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-04-01 12:13:00.047][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:00.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-04-01 12:13:00.055][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-04-01 12:13:00.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-04-01 12:13:00.061][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:00.063][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:13:00.065][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:00.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.084][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.087][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.091][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:00.092][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:00.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.094][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:00.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:00.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.129][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:00.129][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:00.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.132][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:00.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:00.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:00.140][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:00.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.148][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:00.150][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:00.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.152][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.158][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:00.159][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.162][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:00.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.165][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.170][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.171][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.176][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:00.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:00.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:00.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:00.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.209][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:00.210][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:00.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:00.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.219][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:00.220][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:00.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:00.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:00.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:00.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:00.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:00.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.276][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-01 12:13:00.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:00.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:00.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:13:00.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:00.340][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 12:13:00.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:00.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:00.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:00.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:00.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:00.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:00.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:00.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:00.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:00.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:00.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:00.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:00.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:00.986][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:01.075][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:01.166][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:01.170][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-01 12:13:01.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-01 12:13:01.179][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:01.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:01.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:01.185][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:01.306][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:01.394][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:01.396][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-01 12:13:01.400][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-01 12:13:01.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:01.416][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-01 12:13:01.417][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:13:01.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-01 12:13:01.420][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:13:01.436][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:13:01.437][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:13:01.438][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:01.439][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:13:01.440][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:13:01.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:01.456][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-01 12:13:01.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:01.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:01.462][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-01 12:13:01.571][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-01 12:13:01.666][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:01.669][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-01 12:13:01.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-01 12:13:01.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-01 12:13:01.678][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:01.679][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:13:01.681][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:01.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:01.701][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.702][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.705][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.712][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:01.712][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:01.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.714][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.740][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:01.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:01.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.744][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:01.745][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:01.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.747][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:01.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:01.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.752][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:01.753][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:01.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.755][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:01.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:01.760][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:01.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:01.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.766][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:01.767][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:01.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.768][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.769][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:01.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:01.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.773][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:01.774][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:01.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.775][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.776][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:01.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.780][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.782][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.786][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:01.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:01.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.789][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:01.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:01.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:01.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.796][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.797][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:01.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:01.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.802][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:01.803][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:01.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.805][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:01.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:01.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:01.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:01.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:01.843][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-01 12:13:01.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:01.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:01.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:01.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:01.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:01.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:01.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:01.887][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-01 12:13:01.888][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:13:01.890][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-01 12:13:01.891][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:13:01.892][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:13:01.893][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:13:01.893][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:01.894][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:13:01.895][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:13:01.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:01.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:01.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:01.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:01.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:01.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:01.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:01.911][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-01 12:13:01.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:01.934][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-04-01 12:13:01.937][rule$waitAsNeeded] Wait 0.0490851 second(s).
biodb.TRACE[2025-04-01 12:13:02.140][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-01 12:13:02.242][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-01 12:13:02.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:02.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-01 12:13:02.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-01 12:13:02.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-01 12:13:02.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:02.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:13:02.346][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:02.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.360][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.361][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.363][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.367][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:02.368][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:02.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.370][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.410][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:02.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:02.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.414][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:02.415][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:02.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.416][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:02.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:02.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.421][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:02.422][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:02.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.423][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:02.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:02.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.428][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:02.429][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:02.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:02.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:02.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:02.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:02.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.438][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.439][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:02.440][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:02.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.442][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.443][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:02.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:02.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.447][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.453][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:02.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:02.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.456][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.460][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:02.461][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:02.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:02.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.467][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:02.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:02.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.470][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:02.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:02.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:02.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:02.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:02.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.510][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-01 12:13:02.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.542][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:02.563][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:02.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:13:02.566][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:02.568][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 12:13:02.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.682][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.TRACE[2025-04-01 12:13:02.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.773][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.TRACE[2025-04-01 12:13:02.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.842][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.TRACE[2025-04-01 12:13:02.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.913][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[2025-04-01 12:13:02.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:02.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:02.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:02.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:02.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:02.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:02.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:02.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:02.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:02.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:02.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:03.065][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:03.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 12:13:03.068][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:03.069][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 12:13:03.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.091][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[2025-04-01 12:13:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.143][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[2025-04-01 12:13:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.300][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[2025-04-01 12:13:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.399][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.TRACE[2025-04-01 12:13:03.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.505][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[2025-04-01 12:13:03.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.618][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:03.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:13:03.633][biodb::testThat]
biodb.INFO [2025-04-01 12:13:03.634][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-01 12:13:03.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:03.636][biodb::testThat]
biodb.TRACE[2025-04-01 12:13:03.639][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 12:13:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 12:13:03.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.674][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[2025-04-01 12:13:03.676][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:03.680][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:03.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 12:13:03.682][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:03.683][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 12:13:03.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:03.711][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:03.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 12:13:03.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:03.718][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 12:13:03.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:03.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:03.774][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:03.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.796][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.797][private$selectFields]
biodb.TRACE[2025-04-01 12:13:03.798][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:03.799][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:03.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.803][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.804][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.805][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.807][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.807][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.808][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.809][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.810][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.812][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.813][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:03.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.839][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 12:13:03.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:03.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.859][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.859][private$selectFields]
biodb.TRACE[2025-04-01 12:13:03.869][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:03.870][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:03.871][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.872][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.873][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.874][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.875][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.876][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.877][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.879][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.881][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.883][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.885][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.887][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:03.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.900][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:03.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:03.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:03.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:03.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:03.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:03.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:03.913][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[2025-04-01 12:13:03.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.922][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.923][private$selectFields]
biodb.TRACE[2025-04-01 12:13:03.925][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:03.927][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:03.928][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.930][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.935][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.936][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.942][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:03.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.944][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.947][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.949][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:03.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:03.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.963][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 12:13:03.964][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:03.965][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:03.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:03.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:03.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:04.073][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:04.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:04.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:04.081][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:04.172][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:04.266][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:04.269][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-01 12:13:04.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-01 12:13:04.281][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:04.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:04.286][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:04.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:04.379][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:04.475][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:04.478][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-01 12:13:04.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-01 12:13:04.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.519][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[2025-04-01 12:13:04.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.544][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[2025-04-01 12:13:04.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:04.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:04.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.645][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.TRACE[2025-04-01 12:13:04.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.653][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.654][private$selectFields]
biodb.TRACE[2025-04-01 12:13:04.655][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:04.655][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:04.656][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.657][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.658][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.663][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.664][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.664][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.665][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.668][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.668][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.680][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 12:13:04.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:04.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.735][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.736][private$selectFields]
biodb.TRACE[2025-04-01 12:13:04.737][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:04.738][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:04.738][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.740][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.742][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.742][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.745][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.746][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.756][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.757][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.758][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.760][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.760][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.778][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:04.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.824][private$selectFields]
biodb.TRACE[2025-04-01 12:13:04.826][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:04.828][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:04.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.834][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.835][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.837][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.840][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.842][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.843][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:04.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.849][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.850][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 12:13:04.862][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:04.863][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:04.874][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:04.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:13:04.886][biodb::testThat]
biodb.INFO [2025-04-01 12:13:04.888][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-01 12:13:04.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:04.890][biodb::testThat]
biodb.TRACE[2025-04-01 12:13:04.895][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 12:13:04.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 12:13:04.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:04.936][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:04.941][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:04.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 12:13:04.946][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:04.947][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 12:13:04.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:04.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:04.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:04.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:04.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:04.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:04.981][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:04.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 12:13:04.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:04.987][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 12:13:04.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:04.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:04.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:04.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.050][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:05.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.072][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.073][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.073][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.074][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.076][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.077][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.079][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.082][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.083][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.084][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.087][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.088][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.099][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 12:13:05.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.116][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.117][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.118][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.119][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.120][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.121][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.122][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.124][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.125][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.126][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.129][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.129][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.130][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.132][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.135][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.154][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:05.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.174][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.175][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.177][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.178][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.179][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.187][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.192][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.193][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.196][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.197][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.198][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.200][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.201][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.213][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 12:13:05.213][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:05.214][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:05.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:05.263][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.266][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-01 12:13:05.268][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.270][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-01 12:13:05.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.280][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-01 12:13:05.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.284][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-01 12:13:05.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.322][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[2025-04-01 12:13:05.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.359][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:05.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.386][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.386][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.387][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.388][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.389][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.391][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.394][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.395][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.396][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.399][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.400][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.411][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 12:13:05.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.441][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.442][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.443][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.445][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.447][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.450][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.451][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.452][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.453][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.455][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.456][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.469][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:05.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.490][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.491][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.492][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.492][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.496][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.498][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.500][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.502][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.503][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.505][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.506][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.523][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 12:13:05.525][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:05.527][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:05.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:13:05.548][biodb::testThat]
biodb.INFO [2025-04-01 12:13:05.549][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-01 12:13:05.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:05.551][biodb::testThat]
biodb.TRACE[2025-04-01 12:13:05.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 12:13:05.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 12:13:05.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:05.597][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.600][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 12:13:05.603][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.604][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 12:13:05.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.632][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.635][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 12:13:05.638][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.639][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 12:13:05.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.684][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:05.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.703][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.703][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.704][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.705][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.710][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.710][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.711][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.713][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.714][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.718][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.718][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.729][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 12:13:05.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.748][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.749][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.749][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.750][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.751][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.752][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.753][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.754][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.757][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.758][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.759][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.759][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.760][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.763][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.774][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:05.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.801][private$selectFields]
biodb.TRACE[2025-04-01 12:13:05.802][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:05.803][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:05.803][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.804][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.805][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.807][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.810][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.812][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:05.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.816][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.817][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:05.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.828][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 12:13:05.829][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:05.830][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:05.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.881][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[2025-04-01 12:13:05.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.888][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-01 12:13:05.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.891][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-01 12:13:05.895][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:05.898][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:05.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-01 12:13:05.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:05.901][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-01 12:13:05.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.922][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[2025-04-01 12:13:05.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:05.977][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 12:13:05.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:05.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:05.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:05.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:05.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:05.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:05.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:05.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:05.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:05.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.002][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.003][private$selectFields]
biodb.TRACE[2025-04-01 12:13:06.004][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:06.005][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:06.005][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.006][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.008][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.011][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.013][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.020][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.022][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.025][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.026][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:06.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.038][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 12:13:06.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.061][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.062][private$selectFields]
biodb.TRACE[2025-04-01 12:13:06.063][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:06.064][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:06.065][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.068][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.070][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.071][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.072][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.074][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.075][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.076][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.077][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.080][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.081][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.093][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 12:13:06.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:06.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.116][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.116][private$selectFields]
biodb.TRACE[2025-04-01 12:13:06.117][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 12:13:06.118][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 12:13:06.119][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.120][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.122][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.131][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 12:13:06.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.136][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.137][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 12:13:06.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.150][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 12:13:06.151][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 12:13:06.152][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 12:13:06.188][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:06.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 12:13:06.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 12:13:06.197][biodb::testThat]
biodb.INFO [2025-04-01 12:13:06.199][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-04-01 12:13:06.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:06.201][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:06.203][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-01 12:13:06.205][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:13:06.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-01 12:13:06.210][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:13:06.212][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:13:06.213][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:13:06.215][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:06.217][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:13:06.218][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:13:06.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:06.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-01 12:13:06.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:06.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:06.240][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-01 12:13:06.332][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-01 12:13:06.432][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:06.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-01 12:13:06.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-01 12:13:06.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-01 12:13:06.446][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:06.449][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:13:06.450][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:06.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:06.470][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.471][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.473][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.481][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:06.482][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:06.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.486][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.488][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:06.489][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:06.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.491][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.492][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:06.493][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:06.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.495][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.496][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:06.497][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:06.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.499][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.500][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:06.501][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:06.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.502][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.504][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:06.505][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:06.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.506][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.507][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:06.508][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:06.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.511][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.512][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:06.513][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:06.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.515][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.518][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:06.519][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:06.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.521][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:06.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:06.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.524][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:06.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:06.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:06.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:06.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:06.601][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-01 12:13:06.602][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-01 12:13:06.613][biodb::testThat]
biodb.INFO [2025-04-01 12:13:06.614][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-01 12:13:06.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:06.616][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:06.629][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-01 12:13:06.632][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-01 12:13:06.634][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-01 12:13:06.636][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-01 12:13:06.637][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-04-01 12:13:06.639][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-04-01 12:13:06.640][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:13:06.641][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:06.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:13:06.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:13:06.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:06.662][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-01 12:13:06.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:06.686][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:06.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-01 12:13:06.787][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-01 12:13:06.885][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:06.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-01 12:13:06.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-01 12:13:06.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:06.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:06.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:06.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:06.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:06.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:06.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:06.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-01 12:13:06.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:06.918][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:06.920][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-01 12:13:07.034][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-01 12:13:07.136][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:07.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-01 12:13:07.143][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-01 12:13:07.146][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-04-01 12:13:07.148][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:07.149][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-01 12:13:07.150][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:07.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:07.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:07.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:07.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:07.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:07.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:07.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:07.170][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.172][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.177][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.185][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:07.187][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:07.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.190][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.193][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:07.195][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:07.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.197][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.198][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:07.200][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:07.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.203][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.206][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.226][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.228][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.229][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:07.230][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:07.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.236][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:07.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:07.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.239][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.240][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:07.241][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:07.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.242][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.243][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:07.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:07.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:07.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:07.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:07.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:07.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:07.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:07.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:07.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:07.315][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.316][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.317][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.322][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:07.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:07.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.325][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:07.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:07.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.329][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:07.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:07.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.332][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:07.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:07.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:07.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.339][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:07.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:07.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.344][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.346][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.356][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.357][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.359][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.364][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.370][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:07.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:07.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.376][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.378][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:07.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:07.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.384][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.387][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.392][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:07.393][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:07.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.394][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:07.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:07.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.399][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:07.400][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:07.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.402][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.403][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:07.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:07.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.407][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:07.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:07.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.409][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:07.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:07.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:07.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:07.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:07.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:07.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:07.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:07.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:07.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:07.459][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.461][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.469][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:07.471][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:07.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.473][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.474][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:07.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:07.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.478][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:07.478][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:07.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.480][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:07.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:07.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.485][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:07.486][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:07.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.487][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:07.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:07.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.492][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.493][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.494][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:07.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.499][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.501][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:07.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.505][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:07.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:07.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.508][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:07.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:07.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.515][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:07.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.527][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:07.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:07.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.531][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:07.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:07.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:07.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:07.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.540][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:07.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:07.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.545][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:07.547][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:07.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.550][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:07.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:07.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:07.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:07.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:07.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:07.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:07.632][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-01 12:13:07.633][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-01 12:13:07.634][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-01 12:13:07.653][biodb::testThat]
biodb.INFO [2025-04-01 12:13:07.654][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-04-01 12:13:07.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:07.656][biodb::testThat]
biodb.INFO [2025-04-01 12:13:07.686][biodb::testThat]
biodb.INFO [2025-04-01 12:13:07.687][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-04-01 12:13:07.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:07.689][biodb::testThat]
biodb.INFO [2025-04-01 12:13:07.701][biodb::testThat]
biodb.INFO [2025-04-01 12:13:07.702][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-04-01 12:13:07.703][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:07.704][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:07.707][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:07.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:07.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:07.736][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:07.982][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:08.145][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:08.148][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-01 12:13:08.154][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-01 12:13:08.169][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:08.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:08.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:08.173][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:08.174][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:08.174][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:08.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:08.176][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 12:13:08.178][biodb::testThat]
biodb.INFO [2025-04-01 12:13:08.179][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-01 12:13:08.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:08.183][biodb::testThat]
biodb.ERROR[2025-04-01 12:13:08.198][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-01 12:13:08.217][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-01 12:13:08.237][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 12:13:08.241][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 12:13:08.242][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 12:13:08.243][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 12:13:08.244][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.245][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.247][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.248][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.INFO [2025-04-01 12:13:08.259][biodb::testContext]
biodb.INFO [2025-04-01 12:13:08.260][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:08.261][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-01 12:13:08.262][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:08.263][biodb::testContext]
biodb.INFO [2025-04-01 12:13:08.265][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:08.267][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:08.273][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:08.274][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 12:13:08.299][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.305][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 12:13:08.306][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.309][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 12:13:08.310][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.313][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 12:13:08.314][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 12:13:08.315][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 12:13:08.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.318][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 12:13:08.319][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 12:13:08.320][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.323][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 12:13:08.324][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 12:13:08.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.327][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 12:13:08.327][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 12:13:08.328][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 12:13:08.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.331][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 12:13:08.332][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.337][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 12:13:08.338][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 12:13:08.341][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 12:13:08.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.345][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:08.346][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 12:13:08.347][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 12:13:08.348][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 12:13:08.349][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 12:13:08.350][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 12:13:08.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.353][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 12:13:08.353][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 12:13:08.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.358][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 12:13:08.361][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 12:13:08.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.364][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 12:13:08.366][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 12:13:08.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.371][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 12:13:08.372][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 12:13:08.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.375][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 12:13:08.376][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 12:13:08.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.379][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:08.379][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 12:13:08.401][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 12:13:08.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.407][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 12:13:08.408][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 12:13:08.409][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 12:13:08.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.412][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 12:13:08.414][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.415][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 12:13:08.416][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:08.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.419][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.419][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.421][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:08.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:08.423][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.424][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 12:13:08.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:08.425][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:08.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:08.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:08.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:08.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:08.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:08.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:08.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.472][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.473][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:08.474][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:08.475][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.476][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.477][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 12:13:08.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.479][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:08.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:08.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.483][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.484][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.485][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:08.486][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:08.487][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.488][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 12:13:08.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:08.489][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.491][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:08.491][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:08.491][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:08.491][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:08.491][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:08.492][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:08.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.495][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:08.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.497][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.498][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.498][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:08.499][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:08.500][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.501][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.502][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 12:13:08.503][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.504][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 12:13:08.505][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.506][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:08.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.510][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:08.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:08.512][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.512][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 12:13:08.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:08.518][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.520][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.521][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:08.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.524][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:08.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.526][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.527][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.528][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:08.529][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:08.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.530][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.531][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 12:13:08.533][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.534][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:08.535][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.535][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:08.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.539][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:08.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:08.541][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.542][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 12:13:08.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:08.543][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:08.545][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:08.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.551][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:08.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:08.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:08.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:08.560][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:08.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:08.563][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:08.564][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:08.567][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:08.568][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.622][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[2025-04-01 12:13:08.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.628][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[2025-04-01 12:13:08.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.667][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[2025-04-01 12:13:08.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.674][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[2025-04-01 12:13:08.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.679][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[2025-04-01 12:13:08.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.684][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[2025-04-01 12:13:08.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.688][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[2025-04-01 12:13:08.689][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 12:13:08.690][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 12:13:08.691][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 12:13:08.692][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 12:13:08.693][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:08.695][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 12:13:08.696][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:08.697][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:08.698][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 12:13:08.699][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 12:13:08.700][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:08.703][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 12:13:08.704][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:08.707][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:08.709][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 12:13:08.710][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 12:13:08.711][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 12:13:08.713][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 12:13:08.714][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:08.715][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 12:13:08.716][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 12:13:08.718][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 12:13:08.720][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 12:13:08.722][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 12:13:08.723][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 12:13:08.724][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 12:13:08.725][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 12:13:08.726][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 12:13:08.728][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 12:13:08.729][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 12:13:08.730][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 12:13:08.731][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 12:13:08.732][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 12:13:08.735][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 12:13:08.738][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 12:13:08.740][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 12:13:08.741][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 12:13:08.743][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 12:13:08.744][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 12:13:08.769][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 12:13:08.771][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 12:13:08.772][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 12:13:08.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 12:13:08.775][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 12:13:08.776][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 12:13:08.777][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 12:13:08.779][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 12:13:08.780][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 12:13:08.782][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 12:13:08.783][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 12:13:08.784][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 12:13:08.785][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 12:13:08.787][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 12:13:08.788][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 12:13:08.790][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 12:13:08.792][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 12:13:08.794][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 12:13:08.796][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 12:13:08.797][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 12:13:08.798][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 12:13:08.799][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 12:13:08.800][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 12:13:08.802][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 12:13:08.803][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 12:13:08.804][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 12:13:08.805][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 12:13:08.806][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:08.807][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:08.809][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 12:13:08.810][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 12:13:08.811][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 12:13:08.814][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 12:13:08.816][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 12:13:08.818][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 12:13:08.819][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 12:13:08.820][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 12:13:08.822][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 12:13:08.823][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 12:13:08.824][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 12:13:08.825][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 12:13:08.827][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 12:13:08.828][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 12:13:08.829][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 12:13:08.830][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 12:13:08.832][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:08.833][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:08.834][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.835][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.842][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[2025-04-01 12:13:08.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.847][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.DEBUG[2025-04-01 12:13:08.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.930][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[2025-04-01 12:13:08.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:08.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:08.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:08.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:08.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:08.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:08.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.002][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:09.003][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 12:13:09.005][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:09.006][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:09.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.010][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.010][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.011][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 12:13:09.012][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 12:13:09.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:09.016][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.018][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 12:13:09.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 12:13:09.021][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 12:13:09.023][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:09.024][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:09.024][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:09.024][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:09.025][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 12:13:09.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:09.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:09.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:09.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:09.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:09.030][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.031][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:09.031][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 12:13:09.032][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:09.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:09.033][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.034][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 12:13:09.034][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 12:13:09.036][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:09.037][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:09.039][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 12:13:09.040][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:09.041][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:09.043][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:09.046][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 12:13:09.047][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 12:13:09.048][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 12:13:09.049][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 12:13:09.050][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:09.051][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:09.052][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 12:13:09.053][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 12:13:09.055][biodb::testThat]
biodb.INFO [2025-04-01 12:13:09.056][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-04-01 12:13:09.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:09.057][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:09.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 12:13:09.066][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.090][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 12:13:09.094][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.097][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 12:13:09.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.108][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-01 12:13:09.110][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.112][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-01 12:13:09.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.130][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-01 12:13:09.136][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.138][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-01 12:13:09.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.192][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-01 12:13:09.194][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.195][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-01 12:13:09.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.212][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.213][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-01 12:13:09.214][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.215][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-01 12:13:09.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.232][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[2025-04-01 12:13:09.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.243][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.DEBUG[2025-04-01 12:13:09.248][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.257][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-01 12:13:09.259][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.260][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-01 12:13:09.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-01 12:13:09.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.281][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-01 12:13:09.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:09.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-04-01 12:13:09.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:09.304][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-04-01 12:13:09.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 12:13:09.322][biodb::testThat]
biodb.INFO [2025-04-01 12:13:09.323][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-04-01 12:13:09.324][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:09.325][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:09.328][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:09.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:09.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:09.481][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:09.573][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:09.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-01 12:13:09.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-01 12:13:09.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.599][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:09.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:09.605][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:09.607][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:09.703][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:09.807][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:09.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-01 12:13:09.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-01 12:13:09.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:09.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 12:13:09.835][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 12:13:09.836][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 12:13:09.837][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 12:13:09.838][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 12:13:09.839][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:09.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:09.840][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:09.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:09.842][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 12:13:09.847][biodb::testContext]
biodb.INFO [2025-04-01 12:13:09.848][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:09.849][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-01 12:13:09.850][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:09.851][biodb::testContext]
biodb.INFO [2025-04-01 12:13:09.853][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:09.855][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:09.859][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:09.861][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 12:13:09.862][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.866][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 12:13:09.867][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.869][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[2025-04-01 12:13:09.869][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 12:13:09.870][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.874][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 12:13:09.876][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 12:13:09.877][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 12:13:09.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.881][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 12:13:09.882][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 12:13:09.883][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.888][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 12:13:09.890][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 12:13:09.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.893][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[2025-04-01 12:13:09.894][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 12:13:09.895][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 12:13:09.896][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 12:13:09.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.899][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 12:13:09.900][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.904][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 12:13:09.905][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 12:13:09.906][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 12:13:09.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.911][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:09.912][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 12:13:09.913][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 12:13:09.914][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 12:13:09.915][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 12:13:09.916][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 12:13:09.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.918][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 12:13:09.919][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 12:13:09.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.922][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 12:13:09.923][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 12:13:09.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.926][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 12:13:09.927][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 12:13:09.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.930][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 12:13:09.932][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 12:13:09.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.937][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 12:13:09.938][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 12:13:09.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.942][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:09.943][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 12:13:09.966][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 12:13:09.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.969][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 12:13:09.970][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 12:13:09.971][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 12:13:09.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:09.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:09.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:09.975][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 12:13:09.977][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:09.979][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 12:13:09.980][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:09.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.983][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:09.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.985][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:09.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:09.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.987][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 12:13:09.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:09.989][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:09.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:09.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:09.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:09.990][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:09.990][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:09.990][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:09.991][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:09.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:09.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:09.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:09.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:09.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:09.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:09.997][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:09.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:09.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:09.999][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.000][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.001][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 12:13:10.002][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.003][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:10.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.008][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:10.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.011][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.012][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 12:13:10.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.013][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.014][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.015][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:10.015][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:10.015][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:10.015][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:10.015][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:10.016][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.018][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.021][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.023][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.024][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.025][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 12:13:10.027][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.028][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 12:13:10.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.034][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:10.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.035][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.037][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 12:13:10.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.038][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.040][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.042][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.049][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.053][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.054][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 12:13:10.055][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.056][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:10.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:10.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.063][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.064][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 12:13:10.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.066][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.067][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.073][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.074][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.074][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.075][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.076][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.077][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.078][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:10.079][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.136][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.DEBUG[2025-04-01 12:13:10.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.139][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[2025-04-01 12:13:10.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.159][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 12:13:10.161][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 12:13:10.163][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 12:13:10.164][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 12:13:10.165][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:10.166][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 12:13:10.168][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:10.169][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:10.170][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 12:13:10.171][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 12:13:10.172][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:10.174][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 12:13:10.175][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:10.176][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:10.177][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 12:13:10.178][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 12:13:10.179][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 12:13:10.181][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 12:13:10.182][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:10.183][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 12:13:10.184][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 12:13:10.185][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 12:13:10.186][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 12:13:10.188][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 12:13:10.189][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 12:13:10.190][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 12:13:10.191][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 12:13:10.192][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 12:13:10.193][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 12:13:10.195][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 12:13:10.196][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 12:13:10.197][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 12:13:10.198][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 12:13:10.199][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 12:13:10.200][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 12:13:10.201][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 12:13:10.203][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 12:13:10.204][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 12:13:10.205][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 12:13:10.206][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 12:13:10.208][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 12:13:10.209][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 12:13:10.210][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 12:13:10.211][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 12:13:10.213][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 12:13:10.214][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 12:13:10.215][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 12:13:10.216][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 12:13:10.217][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 12:13:10.218][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 12:13:10.220][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 12:13:10.221][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 12:13:10.222][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 12:13:10.224][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 12:13:10.225][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 12:13:10.226][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 12:13:10.227][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 12:13:10.228][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 12:13:10.230][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 12:13:10.231][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 12:13:10.232][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 12:13:10.233][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 12:13:10.234][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 12:13:10.235][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 12:13:10.237][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 12:13:10.238][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 12:13:10.241][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:10.242][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:10.244][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 12:13:10.245][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 12:13:10.246][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 12:13:10.248][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 12:13:10.249][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 12:13:10.250][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 12:13:10.253][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 12:13:10.254][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 12:13:10.256][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 12:13:10.258][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 12:13:10.259][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 12:13:10.260][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 12:13:10.261][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 12:13:10.263][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 12:13:10.264][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 12:13:10.265][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 12:13:10.267][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:10.268][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:10.269][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.270][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.276][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[2025-04-01 12:13:10.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.294][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[2025-04-01 12:13:10.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.301][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[2025-04-01 12:13:10.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.365][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.DEBUG[2025-04-01 12:13:10.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.371][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[2025-04-01 12:13:10.373][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:10.375][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 12:13:10.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.377][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.378][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.380][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.382][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.383][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 12:13:10.384][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 12:13:10.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.386][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 12:13:10.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 12:13:10.388][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 12:13:10.389][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.390][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:10.390][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:10.390][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:10.391][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 12:13:10.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.393][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.399][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.400][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:10.400][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 12:13:10.401][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.402][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.402][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.403][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 12:13:10.403][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 12:13:10.404][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:10.406][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:10.407][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 12:13:10.409][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:10.410][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:10.411][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:10.414][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 12:13:10.415][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 12:13:10.416][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 12:13:10.418][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 12:13:10.419][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:10.420][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:10.421][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 12:13:10.422][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 12:13:10.423][biodb::testThat]
biodb.INFO [2025-04-01 12:13:10.424][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-01 12:13:10.425][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:10.425][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:10.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 12:13:10.432][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:10.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 12:13:10.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:10.436][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 12:13:10.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:10.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:10.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:10.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 12:13:10.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 12:13:10.646][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:10.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-01 12:13:10.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-01 12:13:10.662][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 12:13:10.663][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 12:13:10.664][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 12:13:10.665][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 12:13:10.666][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:10.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:10.667][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.669][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 12:13:10.674][biodb::testContext]
biodb.INFO [2025-04-01 12:13:10.675][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:10.676][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-01 12:13:10.677][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 12:13:10.677][biodb::testContext]
biodb.INFO [2025-04-01 12:13:10.680][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:10.681][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:10.686][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:10.687][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 12:13:10.688][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.690][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[2025-04-01 12:13:10.691][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 12:13:10.692][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.695][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 12:13:10.696][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.699][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 12:13:10.699][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 12:13:10.700][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 12:13:10.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.703][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 12:13:10.704][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 12:13:10.705][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.707][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 12:13:10.708][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 12:13:10.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.711][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 12:13:10.712][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 12:13:10.713][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 12:13:10.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.715][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[2025-04-01 12:13:10.716][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 12:13:10.717][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.719][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 12:13:10.720][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 12:13:10.721][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 12:13:10.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.724][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:10.725][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 12:13:10.726][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 12:13:10.726][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 12:13:10.727][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 12:13:10.728][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 12:13:10.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.731][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 12:13:10.732][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 12:13:10.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.735][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 12:13:10.736][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 12:13:10.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.739][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 12:13:10.740][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 12:13:10.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.744][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 12:13:10.746][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 12:13:10.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.749][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 12:13:10.750][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 12:13:10.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.755][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 12:13:10.756][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 12:13:10.774][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 12:13:10.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.778][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 12:13:10.778][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 12:13:10.779][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 12:13:10.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.783][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 12:13:10.785][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.786][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 12:13:10.787][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.788][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.790][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.791][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.792][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:10.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.794][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.794][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 12:13:10.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.796][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.797][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.798][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:10.798][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:10.798][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:10.798][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:10.798][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:10.800][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.806][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.810][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.811][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 12:13:10.813][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.814][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:10.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.821][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:10.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.823][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.824][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 12:13:10.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.825][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.826][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.827][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:10.827][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:10.827][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:10.827][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 12:13:10.827][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 12:13:10.828][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.830][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.833][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.833][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.837][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.838][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 12:13:10.839][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.841][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 12:13:10.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 12:13:10.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.849][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.850][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 12:13:10.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.852][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.852][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.853][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.854][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.859][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.860][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.861][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.862][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.863][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.864][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 12:13:10.865][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.866][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 12:13:10.867][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:10.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.869][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.870][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.872][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 12:13:10.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:10.873][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.876][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 12:13:10.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:10.878][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:10.881][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 12:13:10.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.884][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:10.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:10.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:10.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:10.887][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:10.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:10.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:10.890][self$setPropertyValue]
biodb.DEBUG[2025-04-01 12:13:10.892][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:10.892][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.893][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[2025-04-01 12:13:10.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.904][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[2025-04-01 12:13:10.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.912][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[2025-04-01 12:13:10.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.915][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[2025-04-01 12:13:10.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.919][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[2025-04-01 12:13:10.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.949][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[2025-04-01 12:13:10.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:10.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:10.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:10.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:10.972][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 12:13:10.974][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 12:13:10.975][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 12:13:10.977][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 12:13:10.978][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:10.979][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 12:13:10.980][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:10.982][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:10.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 12:13:10.984][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 12:13:10.985][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:10.986][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 12:13:10.987][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 12:13:10.989][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 12:13:10.990][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 12:13:10.991][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 12:13:10.992][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 12:13:10.994][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 12:13:10.995][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:10.996][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 12:13:10.997][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 12:13:10.998][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 12:13:11.000][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 12:13:11.001][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 12:13:11.002][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 12:13:11.003][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 12:13:11.004][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 12:13:11.005][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 12:13:11.007][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 12:13:11.008][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 12:13:11.009][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 12:13:11.010][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 12:13:11.011][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 12:13:11.013][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 12:13:11.016][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 12:13:11.017][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 12:13:11.019][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 12:13:11.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 12:13:11.022][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 12:13:11.023][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 12:13:11.024][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 12:13:11.026][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 12:13:11.028][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 12:13:11.029][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 12:13:11.030][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 12:13:11.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 12:13:11.035][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 12:13:11.036][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 12:13:11.038][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 12:13:11.039][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 12:13:11.040][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 12:13:11.041][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 12:13:11.042][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 12:13:11.043][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 12:13:11.045][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 12:13:11.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 12:13:11.047][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 12:13:11.048][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 12:13:11.049][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 12:13:11.050][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 12:13:11.051][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 12:13:11.053][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 12:13:11.054][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 12:13:11.055][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 12:13:11.056][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 12:13:11.057][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 12:13:11.058][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:11.060][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:11.061][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 12:13:11.062][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 12:13:11.063][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 12:13:11.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 12:13:11.066][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 12:13:11.067][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 12:13:11.068][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 12:13:11.069][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 12:13:11.070][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 12:13:11.071][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 12:13:11.072][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 12:13:11.073][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 12:13:11.075][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 12:13:11.076][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 12:13:11.077][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 12:13:11.078][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 12:13:11.080][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 12:13:11.081][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 12:13:11.082][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.083][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.084][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[2025-04-01 12:13:11.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.124][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[2025-04-01 12:13:11.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.148][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[2025-04-01 12:13:11.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.163][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[2025-04-01 12:13:11.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 12:13:11.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.188][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 12:13:11.191][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 12:13:11.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:11.194][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 12:13:11.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:11.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 12:13:11.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:11.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 12:13:11.198][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:11.199][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 12:13:11.200][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 12:13:11.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 12:13:11.202][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:11.202][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 12:13:11.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 12:13:11.204][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 12:13:11.205][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 12:13:11.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 12:13:11.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 12:13:11.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 12:13:11.207][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 12:13:11.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:11.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:11.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 12:13:11.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 12:13:11.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 12:13:11.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 12:13:11.213][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:11.213][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 12:13:11.213][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 12:13:11.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 12:13:11.217][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 12:13:11.218][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 12:13:11.218][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 12:13:11.219][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 12:13:11.224][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 12:13:11.227][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 12:13:11.233][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 12:13:11.235][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 12:13:11.237][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 12:13:11.240][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 12:13:11.241][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 12:13:11.242][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 12:13:11.244][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 12:13:11.245][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:11.246][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 12:13:11.247][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 12:13:11.248][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 12:13:11.249][biodb::testThat]
biodb.INFO [2025-04-01 12:13:11.250][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-01 12:13:11.251][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 12:13:11.251][biodb::testThat]
biodb.DEBUG[2025-04-01 12:13:11.254][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 12:13:11.258][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:11.260][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 12:13:11.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:11.266][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 12:13:11.270][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 12:13:11.273][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 12:13:11.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-01 12:13:11.275][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 12:13:11.277][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-01 12:13:11.281][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-01 12:13:11.282][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 12:13:11.284][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-01 12:13:11.285][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 12:13:11.286][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 12:13:11.287][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 12:13:11.289][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 12:13:11.290][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 12:13:11.291][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 12:13:11.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:11.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:11.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:11.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:11.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:11.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:11.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 12:13:11.381][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-01 12:13:11.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 12:13:11.385][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 12:13:11.387][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-01 12:13:12.416][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-01 12:13:12.683][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 12:13:12.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-01 12:13:12.690][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-01 12:13:12.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-01 12:13:12.694][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 12:13:12.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 12:13:12.697][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 12:13:12.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 12:13:12.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:12.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:12.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:12.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:12.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:12.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 12:13:12.715][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.718][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.722][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:12.723][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:12.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 12:13:12.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 12:13:12.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.755][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:12.756][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:12.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.757][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 12:13:12.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 12:13:12.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.763][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 12:13:12.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 12:13:12.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.768][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 12:13:12.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 12:13:12.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.774][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:12.775][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:12.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.777][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.778][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:12.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 12:13:12.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.782][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:12.782][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:12.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.784][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.785][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 12:13:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 12:13:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.789][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:12.790][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:12.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.791][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 12:13:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.796][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:12.797][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:12.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.798][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 12:13:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 12:13:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.803][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:12.804][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:12.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.806][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.807][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 12:13:12.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 12:13:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.810][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:12.811][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:12.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.813][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 12:13:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 12:13:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 12:13:12.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 12:13:12.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 12:13:12.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 12:13:12.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 12:13:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 12:13:12.855][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-01 12:13:12.860][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 12:13:12.861][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 12:13:12.862][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 12:13:12.863][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 12:13:12.864][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 12:13:12.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 12:13:12.866][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 12:13:12.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 12:13:12.868][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 12:13:12.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
>
> proc.time()
user system elapsed
20.515 1.435 31.336
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.204 | 1.103 | 4.869 | |
| ChebiEntry | 0.354 | 0.020 | 0.389 | |