Pierrick Roger
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 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 2025-03-20 12:04 -0400 (Thu, 20 Mar 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" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2025-03-17 21:06:29 -0400 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 21:08:42 -0400 (Mon, 17 Mar 2025) |
| EllapsedTime: 133.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-17 21:07:11.244][biodb::testContext]
biodb.INFO [2025-03-17 21:07:11.246][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:11.247][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-17 21:07:11.248][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:11.249][biodb::testContext]
biodb.INFO [2025-03-17 21:07:11.256][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:11.258][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:11.266][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:11.267][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-17 21:07:11.268][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.272][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-17 21:07:11.293][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.298][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-17 21:07:11.299][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.303][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-17 21:07:11.304][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-17 21:07:11.305][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-17 21:07:11.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.308][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-17 21:07:11.310][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-17 21:07:11.311][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.314][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-17 21:07:11.316][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-17 21:07:11.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.319][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-17 21:07:11.320][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-17 21:07:11.321][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-17 21:07:11.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.325][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-17 21:07:11.327][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.330][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-17 21:07:11.331][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-17 21:07:11.332][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-17 21:07:11.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.336][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:11.337][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-17 21:07:11.338][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-17 21:07:11.339][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-17 21:07:11.340][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-17 21:07:11.342][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-17 21:07:11.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.344][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[2025-03-17 21:07:11.345][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-17 21:07:11.346][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-17 21:07:11.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.350][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-17 21:07:11.351][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-17 21:07:11.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.354][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.DEBUG[2025-03-17 21:07:11.355][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-17 21:07:11.356][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-17 21:07:11.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.360][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-17 21:07:11.361][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-17 21:07:11.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.365][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-17 21:07:11.366][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-17 21:07:11.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.370][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:11.371][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-17 21:07:11.375][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-17 21:07:11.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.378][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-17 21:07:11.380][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-17 21:07:11.381][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-17 21:07:11.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.388][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-17 21:07:11.425][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.481][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-17 21:07:11.483][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.484][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:11.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:11.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:11.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.492][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-17 21:07:11.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:11.494][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.496][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:11.496][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:11.496][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:11.496][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:11.496][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:11.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:11.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:11.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.504][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:11.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:11.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.509][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.510][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-17 21:07:11.512][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.513][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:11.514][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.515][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:11.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.517][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.518][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.520][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:11.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:11.522][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.523][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-17 21:07:11.524][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:11.525][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.526][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.527][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:11.527][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:11.527][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:11.527][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:11.527][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:11.528][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:11.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.531][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:11.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.534][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.535][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:11.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:11.538][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.539][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.540][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-17 21:07:11.542][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.543][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-17 21:07:11.544][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:11.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.548][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.549][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.550][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:11.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:11.552][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.553][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-17 21:07:11.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:11.555][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.556][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.557][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.558][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:11.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:11.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.565][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.566][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:11.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:11.567][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.568][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.570][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-17 21:07:11.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.572][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:11.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:11.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.579][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:11.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:11.581][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.582][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-17 21:07:11.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:11.584][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.585][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.586][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.587][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:11.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.590][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:11.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.594][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.595][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:11.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:11.597][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.598][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:11.602][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:11.603][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.680][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-17 21:07:11.685][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-17 21:07:11.687][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-17 21:07:11.688][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-17 21:07:11.690][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:11.691][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-17 21:07:11.692][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:11.694][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:11.695][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-17 21:07:11.696][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-17 21:07:11.698][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:11.699][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-17 21:07:11.700][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:11.702][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:11.703][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-17 21:07:11.705][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-17 21:07:11.706][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-17 21:07:11.707][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-17 21:07:11.709][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:11.710][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-17 21:07:11.711][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-17 21:07:11.713][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-17 21:07:11.714][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-17 21:07:11.716][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-17 21:07:11.717][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-17 21:07:11.718][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-17 21:07:11.720][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-17 21:07:11.721][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-17 21:07:11.722][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-17 21:07:11.724][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-17 21:07:11.725][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-17 21:07:11.726][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-17 21:07:11.728][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-17 21:07:11.729][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-17 21:07:11.735][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-17 21:07:11.736][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-17 21:07:11.738][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-17 21:07:11.739][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-17 21:07:11.740][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-17 21:07:11.741][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-17 21:07:11.743][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-17 21:07:11.744][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-17 21:07:11.745][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-17 21:07:11.747][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-17 21:07:11.748][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-17 21:07:11.749][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-17 21:07:11.750][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-17 21:07:11.752][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-17 21:07:11.753][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-17 21:07:11.754][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-17 21:07:11.755][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-17 21:07:11.757][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-17 21:07:11.758][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-17 21:07:11.759][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-17 21:07:11.761][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-17 21:07:11.762][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-17 21:07:11.763][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-17 21:07:11.765][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-17 21:07:11.766][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-17 21:07:11.767][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-17 21:07:11.769][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-17 21:07:11.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-17 21:07:11.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-17 21:07:11.773][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-17 21:07:11.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-17 21:07:11.775][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-17 21:07:11.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:11.778][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:11.779][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-17 21:07:11.780][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-17 21:07:11.782][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-17 21:07:11.783][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-17 21:07:11.785][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-17 21:07:11.786][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-17 21:07:11.787][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-17 21:07:11.788][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-17 21:07:11.790][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-17 21:07:11.791][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-17 21:07:11.792][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-17 21:07:11.793][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-17 21:07:11.795][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-17 21:07:11.796][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-17 21:07:11.797][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-17 21:07:11.803][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-17 21:07:11.805][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:11.808][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:11.808][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.810][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.865][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[2025-03-17 21:07:11.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:11.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:11.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:11.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:11.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:11.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:11.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:11.913][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:11.922][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-17 21:07:11.924][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.925][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:11.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.930][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.930][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-17 21:07:11.931][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-17 21:07:11.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:11.933][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.934][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-17 21:07:11.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-17 21:07:11.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-17 21:07:11.937][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:11.938][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:11.938][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:11.938][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:11.939][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-17 21:07:11.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:11.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:11.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:11.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:11.945][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:11.945][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-17 21:07:11.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:11.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:11.947][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:11.948][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-17 21:07:11.948][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-17 21:07:11.954][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:11.956][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:11.957][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-17 21:07:11.959][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:11.960][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:11.962][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:11.989][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-17 21:07:11.990][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-17 21:07:11.994][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-17 21:07:11.998][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-17 21:07:12.002][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:12.003][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:12.004][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-17 21:07:12.005][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-17 21:07:12.014][biodb::testThat]
biodb.INFO [2025-03-17 21:07:12.015][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-17 21:07:12.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:12.017][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:12.020][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-17 21:07:12.022][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:12.025][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:12.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:12.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:12.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:12.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:12.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:12.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:12.051][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[2025-03-17 21:07:12.060][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.080][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.113][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.122][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.129][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.137][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.138][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.141][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.145][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:12.146][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.148][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.149][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:12.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.153][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.154][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.156][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.161][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.162][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.169][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:12.170][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.173][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:12.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.177][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.178][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:12.265][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-17 21:07:12.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.313][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:12.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:12.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:12.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:12.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:12.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:12.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:12.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:12.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.421][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.499][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.525][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.526][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.551][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.552][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.576][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.577][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.591][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.602][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.603][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.617][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.628][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.629][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.632][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.654][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.658][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.683][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.687][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.688][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.690][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.713][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.738][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.739][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.741][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.752][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.753][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.755][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.759][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.760][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.766][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.767][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.773][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.774][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.780][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.793][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.800][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.801][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.807][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.808][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.814][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.821][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.822][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.824][ef$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:12.830][biodb::testThat]
biodb.INFO [2025-03-17 21:07:12.831][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-17 21:07:12.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:12.833][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:12.846][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-17 21:07:12.853][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:12.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-17 21:07:12.858][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:12.860][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-17 21:07:12.861][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:12.889][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:12.891][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:12.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:12.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:12.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:12.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:12.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:12.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:12.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:12.903][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.905][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:12.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:12.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.927][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.928][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.930][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.935][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.936][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.939][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:12.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.943][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.944][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:12.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.958][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:12.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.966][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:12.967][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:12.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:12.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:12.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.982][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.984][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:12.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:12.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.990][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:12.991][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.992][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:12.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:12.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:12.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:12.998][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:12.999][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:12.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:13.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:13.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:13.043][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-17 21:07:13.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-17 21:07:13.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-17 21:07:13.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-17 21:07:13.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-17 21:07:13.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-17 21:07:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-17 21:07:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:13.061][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.062][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-17 21:07:13.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.064][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:13.067][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.068][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.070][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:13.071][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-17 21:07:13.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:13.113][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-17 21:07:13.117][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-17 21:07:13.137][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:13.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-17 21:07:13.153][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:13.154][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-17 21:07:13.176][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:13.180][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:13.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:13.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:13.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:13.186][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-17 21:07:13.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:13.198][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:13.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.200][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.201][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.203][ef$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:13.207][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.208][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-17 21:07:13.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.209][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:13.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:13.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:13.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:13.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:13.303][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:13.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:13.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:13.307][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-17 21:07:13.320][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.321][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-17 21:07:13.322][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.323][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:13.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:13.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.365][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.368][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.372][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:13.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:13.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.376][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:13.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:13.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:13.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:13.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:13.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:13.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:13.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:13.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.419][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-17 21:07:13.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-17 21:07:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-17 21:07:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:13.439][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.440][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-17 21:07:13.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.442][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.449][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.450][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-17 21:07:13.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.452][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.459][biodb::testThat]
biodb.INFO [2025-03-17 21:07:13.460][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-17 21:07:13.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:13.462][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:13.465][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-17 21:07:14.200][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-17 21:07:15.424][biodb::testThat]
biodb.INFO [2025-03-17 21:07:15.427][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-17 21:07:15.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:15.431][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:15.871][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-17 21:07:16.292][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.296][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.309][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.316][ef$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:16.322][biodb::testThat]
biodb.INFO [2025-03-17 21:07:16.325][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-17 21:07:16.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:16.330][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:16.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:16.548][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:16.552][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:16.554][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:16.556][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.558][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:16.636][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:16.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:16.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:16.643][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.644][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-17 21:07:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-17 21:07:16.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-17 21:07:16.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:16.692][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:16.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:16.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-17 21:07:16.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-17 21:07:16.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:16.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:16.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:16.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:16.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:16.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:16.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:16.718][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-17 21:07:16.763][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:16.765][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-17 21:07:16.767][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.769][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml".
biodb.DEBUG[2025-03-17 21:07:16.770][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:16.771][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:16.772][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:16.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:16.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:16.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:16.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:16.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:16.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:16.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:16.785][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.786][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.794][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:16.795][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:16.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.798][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:16.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.803][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:16.804][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:16.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.811][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:16.812][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:16.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.814][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:16.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.819][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:16.820][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:16.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:16.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:16.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.826][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:16.827][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:16.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.829][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.830][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:16.831][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.838][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.839][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:16.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.845][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:16.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:16.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:16.854][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:16.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:16.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:16.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.861][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:16.862][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:16.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.865][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:16.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:16.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:16.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:16.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:16.912][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-17 21:07:16.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:16.937][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:16.941][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:16.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-17 21:07:16.943][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.945][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-17 21:07:16.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:16.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:16.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:16.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:16.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:16.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:16.971][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.TRACE[2025-03-17 21:07:16.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:16.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:16.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:16.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:16.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:16.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:16.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:16.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:16.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:16.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:16.993][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-17 21:07:16.994][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:16.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-17 21:07:16.997][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:16.999][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml".
biodb.DEBUG[2025-03-17 21:07:17.000][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.002][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.003][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.016][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.017][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.019][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.024][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.025][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.028][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.032][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.033][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.041][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.042][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.044][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.049][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.050][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.064][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.065][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.068][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.069][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.072][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.085][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.093][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.094][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.097][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.101][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.102][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.148][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-17 21:07:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:17.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:17.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:17.184][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.186][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:17.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:17.221][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-17 21:07:17.222][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:17.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-17 21:07:17.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.227][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml".
biodb.DEBUG[2025-03-17 21:07:17.228][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.229][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.230][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.249][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.258][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.259][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.262][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.263][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.269][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.271][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.272][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.275][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.276][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.278][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.279][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.280][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.283][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.284][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.287][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.288][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.295][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.296][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.299][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.303][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.304][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.361][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-17 21:07:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:17.409][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-17 21:07:17.410][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:17.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-17 21:07:17.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml".
biodb.DEBUG[2025-03-17 21:07:17.419][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.421][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.423][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.444][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.455][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.461][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.502][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.515][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.516][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.521][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.523][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.527][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.533][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.534][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.538][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.540][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.550][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.555][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.563][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.614][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-17 21:07:17.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:17.644][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-17 21:07:17.645][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:17.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-17 21:07:17.648][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.649][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml".
biodb.DEBUG[2025-03-17 21:07:17.650][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.653][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.665][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.666][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.668][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.673][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.674][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.676][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.677][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.678][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.681][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.684][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.685][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.686][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.691][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.692][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.693][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.696][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.706][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.714][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.715][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.764][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-17 21:07:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:17.794][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-17 21:07:17.795][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:17.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-17 21:07:17.797][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.799][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml".
biodb.DEBUG[2025-03-17 21:07:17.800][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.801][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.802][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.815][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.816][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.823][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.824][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.825][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.831][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:17.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:17.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.839][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.840][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:17.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:17.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.847][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.848][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.854][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.855][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.859][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:17.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.862][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.866][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:17.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:17.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:17.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.891][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.892][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:17.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:17.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.899][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.943][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-17 21:07:17.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:17.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:17.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:17.965][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-17 21:07:17.966][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:17.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-17 21:07:17.968][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:17.970][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml".
biodb.DEBUG[2025-03-17 21:07:17.971][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:17.972][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:17.973][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:17.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:17.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:17.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:17.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:17.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:17.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:17.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:17.985][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:17.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.993][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.994][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:17.996][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:17.997][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:17.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:17.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.001][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.002][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.004][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.010][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.011][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.026][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.027][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.030][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.034][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.035][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.038][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.047][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.048][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.055][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.063][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.064][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.066][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.071][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.072][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.116][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-17 21:07:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:18.140][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-17 21:07:18.141][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.142][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-17 21:07:18.144][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.145][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml".
biodb.DEBUG[2025-03-17 21:07:18.146][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.147][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.149][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.162][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.163][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.165][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.170][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.171][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.178][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.179][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.186][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.187][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.195][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.206][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.207][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.210][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.226][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.227][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.233][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.234][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.237][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.241][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.242][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.284][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-17 21:07:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:18.305][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-17 21:07:18.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-17 21:07:18.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.310][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2025-03-17 21:07:18.311][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.312][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.314][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.326][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.333][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.334][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.337][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.340][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.348][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.349][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.355][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.356][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.363][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.367][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.380][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.387][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.388][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.394][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.395][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.402][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.403][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.446][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-17 21:07:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:18.467][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-17 21:07:18.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-17 21:07:18.471][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.472][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2025-03-17 21:07:18.473][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.474][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.475][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.487][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.489][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.495][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.496][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.499][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.503][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.504][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.511][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.511][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.519][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.526][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.527][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.530][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.551][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.562][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.566][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.613][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-17 21:07:18.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:18.634][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-17 21:07:18.635][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-17 21:07:18.638][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.640][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2025-03-17 21:07:18.641][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.642][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.643][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.656][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.657][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.663][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.664][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.666][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.667][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.671][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.674][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.681][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.686][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.695][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.697][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.698][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.699][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.702][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.705][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.718][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.719][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.726][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.727][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.730][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.733][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.777][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-17 21:07:18.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:18.799][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-17 21:07:18.800][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-17 21:07:18.803][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.804][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2025-03-17 21:07:18.805][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.806][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.807][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.819][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.827][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.828][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.835][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:18.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:18.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.842][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:18.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.857][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.858][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:18.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.861][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.862][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.865][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:18.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.869][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.870][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:18.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:18.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:18.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.892][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.893][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.896][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:18.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.901][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:18.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:18.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:18.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.945][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-17 21:07:18.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:18.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:18.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.965][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[2025-03-17 21:07:18.966][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-17 21:07:18.967][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:18.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-17 21:07:18.970][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:18.971][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2025-03-17 21:07:18.972][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:18.973][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:18.974][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:18.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:18.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:18.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:18.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:18.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:18.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:18.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:18.986][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:18.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:18.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.994][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:18.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:18.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:18.998][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:18.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.002][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.003][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.009][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.010][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.014][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.014][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.017][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.018][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.021][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.022][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.024][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.025][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.029][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.030][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.036][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.049][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.057][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.058][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.099][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-17 21:07:19.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:19.121][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-17 21:07:19.122][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:19.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-17 21:07:19.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:19.126][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2025-03-17 21:07:19.127][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:19.129][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:19.130][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:19.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:19.142][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.149][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.150][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.152][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.157][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.158][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.164][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.165][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.168][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.171][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.172][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.173][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.176][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.177][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.183][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.184][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.191][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.200][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.202][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.206][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.284][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-17 21:07:19.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:19.305][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-17 21:07:19.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:19.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-17 21:07:19.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:19.319][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2025-03-17 21:07:19.320][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:19.322][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:19.323][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:19.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:19.335][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.343][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.344][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.350][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.351][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.358][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.366][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.367][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.374][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.377][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.381][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.385][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.393][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.400][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.401][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.404][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.408][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.459][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-17 21:07:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:19.481][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-17 21:07:19.482][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:19.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-17 21:07:19.484][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:19.497][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2025-03-17 21:07:19.498][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:19.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:19.500][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:19.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:19.512][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.520][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.521][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.527][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.528][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.536][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.543][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.544][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.558][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.563][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.564][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.567][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.572][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.580][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.581][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.583][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.589][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.590][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.592][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.593][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.597][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.598][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.664][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-17 21:07:19.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:19.687][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-17 21:07:19.688][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:19.690][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-17 21:07:19.691][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:19.693][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2025-03-17 21:07:19.694][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:19.695][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:19.696][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:19.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:19.709][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.717][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.718][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.725][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.726][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.741][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.749][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.750][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.753][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.754][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.757][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.776][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.777][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.780][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.832][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-17 21:07:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:19.853][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-17 21:07:19.854][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:19.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-17 21:07:19.856][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:19.858][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2025-03-17 21:07:19.859][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:19.860][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:19.861][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:19.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:19.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:19.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:19.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:19.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:19.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:19.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:19.873][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.880][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.881][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.884][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:19.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:19.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.888][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:19.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:19.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:19.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:19.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.903][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.904][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:19.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.910][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.911][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:19.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.914][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.915][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.918][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:19.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.922][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.923][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:19.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.929][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:19.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:19.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.937][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.938][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.940][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.941][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:19.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:19.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.944][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.945][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:19.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:19.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:19.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:19.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:19.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:19.993][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-17 21:07:19.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:19.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:19.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:19.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:20.014][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-17 21:07:20.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:20.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-17 21:07:20.018][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:20.020][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2025-03-17 21:07:20.021][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:20.022][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:20.023][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:20.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.035][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.036][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.042][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.043][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.050][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.072][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.073][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.076][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.077][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.080][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.084][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.092][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.099][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.100][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.103][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.107][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.158][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-17 21:07:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:20.179][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-17 21:07:20.180][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:20.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-17 21:07:20.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:20.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2025-03-17 21:07:20.185][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:20.186][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:20.187][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:20.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.200][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.207][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.211][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.215][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.216][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.218][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.230][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.231][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.238][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.239][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.242][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.242][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.245][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.250][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.257][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.258][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.269][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.322][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-17 21:07:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:20.343][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-17 21:07:20.344][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:20.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-17 21:07:20.347][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:20.348][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2025-03-17 21:07:20.349][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:20.351][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:20.352][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:20.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.364][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.365][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.371][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.372][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.375][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:20.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:20.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.379][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:20.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:20.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.388][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:20.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.395][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.396][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:20.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.403][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.404][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:20.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.407][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.408][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:20.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.415][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.422][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.423][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:20.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:20.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.430][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.431][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.434][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:20.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:20.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.438][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.439][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.441][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.442][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:20.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:20.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:20.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.488][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-17 21:07:20.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:20.521][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:20.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:20.523][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:20.525][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:20.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.588][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.TRACE[2025-03-17 21:07:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.794][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[2025-03-17 21:07:20.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.903][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.TRACE[2025-03-17 21:07:20.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:20.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:20.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:20.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:20.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:20.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:20.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:20.971][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.TRACE[2025-03-17 21:07:20.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:20.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:20.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.041][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:21.045][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:21.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2025-03-17 21:07:21.048][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.049][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2025-03-17 21:07:21.052][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:21.055][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:21.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2025-03-17 21:07:21.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.059][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2025-03-17 21:07:21.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:21.072][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-17 21:07:21.073][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:21.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-17 21:07:21.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.077][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2025-03-17 21:07:21.078][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:21.079][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:21.080][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:21.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.095][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.096][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.102][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:21.103][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:21.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:21.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.110][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:21.111][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:21.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.115][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:21.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:21.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.118][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:21.119][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:21.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:21.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:21.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.134][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.135][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.137][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.148][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:21.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:21.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.152][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:21.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.164][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:21.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:21.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:21.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:21.173][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:21.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.176][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:21.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:21.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:21.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:21.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:21.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:21.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.225][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-17 21:07:21.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:21.268][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-17 21:07:21.269][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:21.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-17 21:07:21.272][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.274][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2025-03-17 21:07:21.275][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:21.276][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:21.277][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:21.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.291][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.297][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:21.298][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:21.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:21.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.305][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:21.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:21.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.308][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:21.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:21.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:21.321][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:21.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:21.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:21.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.328][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.336][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:21.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.340][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:21.341][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:21.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.344][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:21.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:21.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.356][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:21.357][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:21.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:21.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:21.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.364][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:21.365][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:21.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.368][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:21.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:21.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.372][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:21.373][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:21.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:21.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:21.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:21.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:21.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.418][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-17 21:07:21.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:21.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:21.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:21.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.453][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:21.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.465][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[2025-03-17 21:07:21.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.628][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.TRACE[2025-03-17 21:07:21.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.723][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.TRACE[2025-03-17 21:07:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.787][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[2025-03-17 21:07:21.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.879][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.TRACE[2025-03-17 21:07:21.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.900][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.TRACE[2025-03-17 21:07:21.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.952][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:21.955][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:21.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-17 21:07:21.958][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:21.960][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-17 21:07:21.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:21.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:21.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:21.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:21.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:21.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:21.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:21.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:21.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:21.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:21.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.026][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.TRACE[2025-03-17 21:07:22.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.124][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.TRACE[2025-03-17 21:07:22.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.166][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[2025-03-17 21:07:22.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.434][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:22.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:22.445][biodb::testThat]
biodb.INFO [2025-03-17 21:07:22.446][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-17 21:07:22.447][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:22.448][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:22.451][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-17 21:07:22.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-17 21:07:22.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.481][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[2025-03-17 21:07:22.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:22.487][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:22.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-17 21:07:22.489][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:22.491][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-17 21:07:22.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.515][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:22.524][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:22.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-17 21:07:22.526][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:22.528][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-17 21:07:22.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.561][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.TRACE[2025-03-17 21:07:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:22.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.573][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:22.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.593][private$selectFields]
biodb.TRACE[2025-03-17 21:07:22.594][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:22.595][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:22.596][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.597][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.604][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.605][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.606][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.607][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.610][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.631][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-17 21:07:22.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.650][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.651][private$selectFields]
biodb.TRACE[2025-03-17 21:07:22.652][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:22.653][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:22.654][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.655][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.659][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.660][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.662][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.668][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:22.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.681][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:22.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.706][private$selectFields]
biodb.TRACE[2025-03-17 21:07:22.707][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:22.708][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:22.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.710][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.711][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.713][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.717][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.718][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.722][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:22.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.735][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-17 21:07:22.735][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:22.736][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:22.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.825][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.DEBUG[2025-03-17 21:07:22.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:22.831][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:22.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-17 21:07:22.834][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:22.835][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-17 21:07:22.838][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:22.842][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:22.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-17 21:07:22.853][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:22.856][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-17 21:07:22.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.868][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[2025-03-17 21:07:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.910][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.TRACE[2025-03-17 21:07:22.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:22.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:22.946][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:22.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:22.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:22.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:22.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:22.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:22.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:22.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:22.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.987][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.988][private$selectFields]
biodb.TRACE[2025-03-17 21:07:22.989][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:22.989][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:22.990][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:22.991][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.992][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.994][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:22.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:22.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:22.999][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.000][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.004][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.023][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-17 21:07:23.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:23.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:23.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:23.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:23.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:23.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:23.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:23.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.072][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.073][private$selectFields]
biodb.TRACE[2025-03-17 21:07:23.074][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:23.075][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:23.076][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.077][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.080][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.081][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.082][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.085][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.095][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.100][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:23.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.113][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:23.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:23.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:23.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:23.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:23.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:23.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:23.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:23.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.132][private$selectFields]
biodb.TRACE[2025-03-17 21:07:23.133][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:23.134][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:23.135][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.139][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.144][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:23.145][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.146][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.148][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.149][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:23.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-17 21:07:23.162][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:23.168][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:23.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:23.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:23.184][biodb::testThat]
biodb.INFO [2025-03-17 21:07:23.185][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-17 21:07:23.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:23.187][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-17 21:07:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-17 21:07:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:23.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:23.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:23.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:23.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:23.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:23.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:23.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:23.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:23.226][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:23.228][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-17 21:07:23.229][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:23.231][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-17 21:07:23.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:23.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:23.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:23.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:23.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:23.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:23.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:23.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:23.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:23.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:23.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:23.256][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.INFO [2025-03-17 21:07:23.259][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-17 21:07:23.261][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:23.262][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:23.263][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:23.622][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:23.987][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:23.992][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-17 21:07:24.024][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-17 21:07:24.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:24.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:24.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:24.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:24.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:24.087][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:24.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.109][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[2025-03-17 21:07:24.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.118][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.119][private$selectFields]
biodb.TRACE[2025-03-17 21:07:24.120][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:24.121][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:24.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.131][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.136][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.148][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-17 21:07:24.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.167][private$selectFields]
biodb.TRACE[2025-03-17 21:07:24.168][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:24.169][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:24.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.172][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.175][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.176][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.179][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.181][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.184][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:24.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.197][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:24.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:24.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.217][private$selectFields]
biodb.TRACE[2025-03-17 21:07:24.218][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:24.218][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:24.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.225][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.228][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.229][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:24.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.233][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:24.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:24.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.246][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-17 21:07:24.247][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:24.248][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:24.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:24.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:24.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:24.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:24.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:24.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:24.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:24.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:24.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:24.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:24.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:24.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:24.349][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:24.711][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:25.078][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:25.083][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-17 21:07:25.093][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-17 21:07:25.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:25.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:25.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:25.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:25.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:25.845][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-17 21:07:25.849][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-17 21:07:25.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-17 21:07:25.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-17 21:07:25.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:25.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:25.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:25.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:25.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:25.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:25.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:25.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:25.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:25.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:25.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:25.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:25.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:25.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:25.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:25.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:25.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:25.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:25.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:25.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:25.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:25.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:25.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:25.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:25.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:25.960][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:25.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:25.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:25.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:25.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:25.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:25.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:25.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:25.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:25.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:25.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:25.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:25.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:25.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:25.999][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.000][private$selectFields]
biodb.TRACE[2025-03-17 21:07:26.001][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:26.002][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:26.003][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.004][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.007][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.008][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.012][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.013][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:26.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.029][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-17 21:07:26.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:26.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:26.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:26.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:26.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:26.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:26.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:26.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.048][private$selectFields]
biodb.TRACE[2025-03-17 21:07:26.049][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:26.050][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:26.051][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.052][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.056][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.060][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.064][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:26.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.077][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:26.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:26.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:26.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:26.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:26.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:26.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:26.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.096][private$selectFields]
biodb.TRACE[2025-03-17 21:07:26.096][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:26.097][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:26.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.107][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.107][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:26.108][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.109][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.112][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:26.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:26.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.125][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-17 21:07:26.126][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:26.127][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:26.134][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:26.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:26.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:26.141][biodb::testThat]
biodb.INFO [2025-03-17 21:07:26.142][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-17 21:07:26.143][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:26.144][biodb::testThat]
biodb.TRACE[2025-03-17 21:07:26.151][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-17 21:07:26.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-17 21:07:26.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:26.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:26.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:26.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:26.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:26.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:26.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:26.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:26.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:26.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:26.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:26.192][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:26.560][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:26.917][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:26.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-17 21:07:26.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-17 21:07:26.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:26.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:26.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:26.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:26.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:26.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:26.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:26.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:26.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:26.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:26.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:26.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:26.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:27.003][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:27.369][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:27.724][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:27.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-17 21:07:27.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-17 21:07:27.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:27.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:27.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:27.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:27.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:27.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:27.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:27.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:27.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:27.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:27.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:27.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:27.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:27.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:27.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:27.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:27.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:27.785][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:27.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:27.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:27.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:27.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:27.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:27.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:27.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:27.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.808][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.809][private$selectFields]
biodb.TRACE[2025-03-17 21:07:27.810][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:27.811][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:27.812][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.816][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.838][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.839][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.840][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.841][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.844][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.858][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-17 21:07:27.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:27.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:27.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:27.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:27.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:27.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:27.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:27.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.881][private$selectFields]
biodb.TRACE[2025-03-17 21:07:27.882][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:27.883][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:27.884][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.885][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.894][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.899][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:27.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.913][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:27.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:27.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:27.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:27.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:27.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:27.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:27.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:27.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.935][private$selectFields]
biodb.TRACE[2025-03-17 21:07:27.936][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:27.937][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:27.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.944][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.947][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.948][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:27.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.952][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.953][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:27.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.968][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-17 21:07:27.969][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:27.970][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:27.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:27.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:27.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:27.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:28.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:28.036][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:28.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:28.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:28.043][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:28.397][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:28.758][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:28.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-17 21:07:28.769][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-17 21:07:28.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:28.780][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:28.783][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-17 21:07:28.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:28.787][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-17 21:07:28.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:28.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:28.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:28.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.863][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[2025-03-17 21:07:28.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:28.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:28.876][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-17 21:07:28.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.887][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.TRACE[2025-03-17 21:07:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.898][private$selectFields]
biodb.TRACE[2025-03-17 21:07:28.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:28.900][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:28.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.910][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.911][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.916][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:28.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.929][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-17 21:07:28.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:28.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:28.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:28.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:28.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.961][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.962][private$selectFields]
biodb.TRACE[2025-03-17 21:07:28.963][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:28.964][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:28.965][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.970][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.971][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.973][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.975][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:28.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.980][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:28.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:28.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:28.993][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-17 21:07:28.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:28.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:28.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:29.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:29.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:29.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:29.004][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[2025-03-17 21:07:29.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:29.015][private$selectFields]
biodb.TRACE[2025-03-17 21:07:29.015][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-17 21:07:29.016][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-17 21:07:29.017][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:29.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.022][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.023][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:29.027][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-17 21:07:29.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.032][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-17 21:07:29.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.046][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-17 21:07:29.047][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-17 21:07:29.048][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-17 21:07:29.068][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:29.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-17 21:07:29.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:29.075][biodb::testThat]
biodb.INFO [2025-03-17 21:07:29.076][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-17 21:07:29.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:29.078][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:29.080][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-17 21:07:29.081][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:29.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-17 21:07:29.084][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-17 21:07:29.085][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-17 21:07:29.087][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:29.088][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:29.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-17 21:07:29.090][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-17 21:07:29.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:29.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:29.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:29.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:29.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:29.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:29.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:29.104][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-17 21:07:29.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:29.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:29.110][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-17 21:07:29.467][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-17 21:07:29.842][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:29.846][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-17 21:07:29.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-17 21:07:29.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-17 21:07:29.860][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-17 21:07:29.863][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:29.865][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:29.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:29.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:29.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:29.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:29.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:29.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:29.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:29.903][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.904][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.907][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.913][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:29.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:29.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.918][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:29.919][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:29.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.921][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:29.924][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:29.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.927][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:29.928][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:29.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.930][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:29.932][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:29.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.935][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:29.936][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:29.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.939][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:29.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:29.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.941][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.942][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:29.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:29.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.946][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:29.947][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:29.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.950][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:29.951][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:29.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:29.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:29.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:29.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:29.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:29.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:29.991][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-17 21:07:29.992][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-17 21:07:29.999][biodb::testThat]
biodb.INFO [2025-03-17 21:07:30.000][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-17 21:07:30.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:30.002][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:30.010][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-17 21:07:30.011][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-17 21:07:30.012][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-17 21:07:30.019][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-17 21:07:30.021][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-17 21:07:30.023][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-17 21:07:30.024][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:30.025][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:30.027][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-17 21:07:30.028][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-17 21:07:30.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:30.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:30.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:30.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:30.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:30.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:30.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:30.060][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-17 21:07:30.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:30.064][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:30.065][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-17 21:07:30.433][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-17 21:07:30.805][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:30.830][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-17 21:07:30.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-17 21:07:30.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:30.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:30.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:30.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:30.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:30.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:30.847][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[2025-03-17 21:07:30.849][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-17 21:07:30.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:30.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:30.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-17 21:07:31.218][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-17 21:07:31.590][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:31.594][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-17 21:07:31.602][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-17 21:07:31.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:31.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:31.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:31.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:31.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:31.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:31.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:31.629][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-17 21:07:31.634][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:31.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:31.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-17 21:07:32.001][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-17 21:07:32.372][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:32.377][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-17 21:07:32.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-17 21:07:32.391][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-17 21:07:32.395][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-17 21:07:32.398][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-17 21:07:32.401][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:32.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:32.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:32.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:32.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:32.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:32.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:32.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:32.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.432][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.443][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:32.445][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:32.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.449][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:32.450][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:32.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.455][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:32.456][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:32.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.459][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.461][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.464][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.465][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.468][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:32.469][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:32.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.476][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:32.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:32.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.481][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:32.482][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:32.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.485][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:32.486][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:32.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:32.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:32.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:32.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:32.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:32.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:32.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:32.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:32.526][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.527][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.546][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:32.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:32.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.550][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:32.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:32.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.554][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:32.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:32.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.557][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:32.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:32.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:32.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:32.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:32.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:32.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.577][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.578][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.581][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.585][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:32.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:32.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.600][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:32.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:32.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.608][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:32.609][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:32.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.612][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:32.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:32.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.616][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:32.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:32.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.620][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:32.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:32.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:32.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:32.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:32.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:32.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:32.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:32.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:32.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.663][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.668][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:32.669][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:32.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:32.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:32.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.677][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:32.677][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:32.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:32.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:32.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:32.685][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:32.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:32.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:32.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.692][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.693][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:32.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.704][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.706][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.709][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:32.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.713][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:32.714][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:32.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:32.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:32.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.722][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.729][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:32.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:32.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.732][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:32.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:32.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.737][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:32.738][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:32.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.741][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:32.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:32.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:32.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:32.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.747][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.749][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:32.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:32.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:32.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:32.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:32.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:32.812][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-17 21:07:32.813][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-17 21:07:32.814][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-17 21:07:32.826][biodb::testThat]
biodb.INFO [2025-03-17 21:07:32.827][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-17 21:07:32.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:32.829][biodb::testThat]
biodb.INFO [2025-03-17 21:07:32.851][biodb::testThat]
biodb.INFO [2025-03-17 21:07:32.852][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-17 21:07:32.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:32.854][biodb::testThat]
biodb.INFO [2025-03-17 21:07:32.868][biodb::testThat]
biodb.INFO [2025-03-17 21:07:32.869][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-17 21:07:32.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:32.871][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:32.873][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:32.876][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:32.877][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:32.879][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:33.336][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:33.873][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:33.876][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-17 21:07:33.880][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-17 21:07:33.893][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:33.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:33.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:33.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:33.898][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:33.899][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:33.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:33.901][ef$get] fields variable is a list.
biodb.INFO [2025-03-17 21:07:33.902][biodb::testThat]
biodb.INFO [2025-03-17 21:07:33.903][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-17 21:07:33.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:33.905][biodb::testThat]
biodb.ERROR[2025-03-17 21:07:33.922][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-17 21:07:33.942][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-17 21:07:33.958][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-17 21:07:33.960][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-17 21:07:33.961][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-17 21:07:33.962][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-17 21:07:33.963][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:33.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:33.964][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:33.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:33.966][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:33.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-17 21:07:33.977][biodb::testContext]
biodb.INFO [2025-03-17 21:07:33.978][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:33.978][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-17 21:07:33.979][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:33.980][biodb::testContext]
biodb.INFO [2025-03-17 21:07:33.982][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:33.984][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:33.988][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:33.989][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-17 21:07:33.990][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-17 21:07:33.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:33.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:33.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:33.993][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-17 21:07:33.995][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-17 21:07:33.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:33.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:33.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:33.998][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-17 21:07:33.999][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-17 21:07:34.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.002][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-17 21:07:34.003][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-17 21:07:34.004][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-17 21:07:34.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.008][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-17 21:07:34.009][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-17 21:07:34.010][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-17 21:07:34.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.013][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-17 21:07:34.014][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-17 21:07:34.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.018][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-17 21:07:34.019][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-17 21:07:34.020][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-17 21:07:34.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.023][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-17 21:07:34.024][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-17 21:07:34.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.028][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-17 21:07:34.029][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-17 21:07:34.030][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-17 21:07:34.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.046][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:34.047][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-17 21:07:34.048][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-17 21:07:34.050][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-17 21:07:34.051][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-17 21:07:34.052][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-17 21:07:34.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.055][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-17 21:07:34.056][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-17 21:07:34.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.060][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-17 21:07:34.061][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-17 21:07:34.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.064][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-17 21:07:34.065][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-17 21:07:34.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.069][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-17 21:07:34.070][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-17 21:07:34.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.073][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-17 21:07:34.074][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-17 21:07:34.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.078][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:34.079][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-17 21:07:34.081][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-17 21:07:34.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.085][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-17 21:07:34.086][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-17 21:07:34.087][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-17 21:07:34.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.089][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[2025-03-17 21:07:34.091][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-17 21:07:34.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.093][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-17 21:07:34.094][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.095][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:34.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.097][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.099][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.100][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:34.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:34.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.103][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-17 21:07:34.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:34.105][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.107][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:34.107][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:34.107][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:34.107][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:34.107][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:34.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:34.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:34.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.115][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:34.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:34.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.118][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.119][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-17 21:07:34.121][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.122][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:34.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.124][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:34.125][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.128][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.129][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:34.130][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:34.131][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.132][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-17 21:07:34.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:34.134][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.134][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.135][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:34.135][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:34.135][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:34.135][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:34.135][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:34.136][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:34.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.139][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:34.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.142][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.143][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:34.144][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:34.145][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.146][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.147][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-17 21:07:34.149][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-17 21:07:34.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:34.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.156][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.157][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:34.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:34.159][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.160][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-17 21:07:34.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:34.162][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.164][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:34.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.168][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:34.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.171][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.172][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.173][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:34.173][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:34.174][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.175][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.176][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-17 21:07:34.178][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.179][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:34.180][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.181][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:34.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.183][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.184][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:34.187][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:34.187][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.188][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-17 21:07:34.189][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:34.190][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.191][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.192][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.193][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:34.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.196][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:34.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.199][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.200][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:34.201][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:34.208][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.209][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:34.210][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:34.212][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.243][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[2025-03-17 21:07:34.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.286][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[2025-03-17 21:07:34.287][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-17 21:07:34.289][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-17 21:07:34.290][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-17 21:07:34.292][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-17 21:07:34.293][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:34.294][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-17 21:07:34.296][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:34.297][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:34.298][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-17 21:07:34.300][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-17 21:07:34.301][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:34.302][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-17 21:07:34.304][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:34.305][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:34.306][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-17 21:07:34.308][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-17 21:07:34.309][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-17 21:07:34.310][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-17 21:07:34.311][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:34.313][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-17 21:07:34.314][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-17 21:07:34.315][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-17 21:07:34.317][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-17 21:07:34.318][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-17 21:07:34.319][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-17 21:07:34.321][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-17 21:07:34.322][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-17 21:07:34.323][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-17 21:07:34.325][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-17 21:07:34.326][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-17 21:07:34.327][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-17 21:07:34.329][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-17 21:07:34.330][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-17 21:07:34.332][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-17 21:07:34.333][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-17 21:07:34.334][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-17 21:07:34.335][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-17 21:07:34.337][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-17 21:07:34.338][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-17 21:07:34.339][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-17 21:07:34.341][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-17 21:07:34.342][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-17 21:07:34.343][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-17 21:07:34.345][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-17 21:07:34.346][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-17 21:07:34.347][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-17 21:07:34.349][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-17 21:07:34.350][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-17 21:07:34.351][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-17 21:07:34.353][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-17 21:07:34.354][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-17 21:07:34.355][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-17 21:07:34.357][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-17 21:07:34.358][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-17 21:07:34.365][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-17 21:07:34.366][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-17 21:07:34.368][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-17 21:07:34.369][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-17 21:07:34.371][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-17 21:07:34.372][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-17 21:07:34.373][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-17 21:07:34.375][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-17 21:07:34.376][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-17 21:07:34.378][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-17 21:07:34.379][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-17 21:07:34.380][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-17 21:07:34.382][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:34.383][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:34.384][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-17 21:07:34.386][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-17 21:07:34.387][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-17 21:07:34.388][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-17 21:07:34.390][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-17 21:07:34.391][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-17 21:07:34.392][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-17 21:07:34.394][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-17 21:07:34.395][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-17 21:07:34.396][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-17 21:07:34.398][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-17 21:07:34.399][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-17 21:07:34.400][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-17 21:07:34.402][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-17 21:07:34.403][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-17 21:07:34.405][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-17 21:07:34.406][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:34.407][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:34.408][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.410][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:34.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:34.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:34.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:34.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:34.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:34.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:34.514][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:34.515][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-17 21:07:34.524][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.525][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.528][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:34.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.531][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.532][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-17 21:07:34.533][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-17 21:07:34.534][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:34.535][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.536][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-17 21:07:34.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-17 21:07:34.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-17 21:07:34.540][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:34.541][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:34.541][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:34.541][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:34.542][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-17 21:07:34.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:34.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:34.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:34.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:34.549][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:34.549][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-17 21:07:34.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:34.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:34.552][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:34.553][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-17 21:07:34.553][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-17 21:07:34.554][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:34.556][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:34.557][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-17 21:07:34.559][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:34.560][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:34.562][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:34.566][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-17 21:07:34.567][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-17 21:07:34.568][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-17 21:07:34.569][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-17 21:07:34.571][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:34.572][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:34.573][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-17 21:07:34.574][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-17 21:07:34.575][biodb::testThat]
biodb.INFO [2025-03-17 21:07:34.576][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-17 21:07:34.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:34.578][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:34.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-17 21:07:34.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:34.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:34.588][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-17 21:07:34.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-17 21:07:35.440][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:35.442][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-17 21:07:35.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-17 21:07:35.450][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:35.453][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:35.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:35.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:35.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:36.189][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:36.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-17 21:07:36.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-17 21:07:36.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:36.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:36.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:36.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:36.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:36.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:36.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:36.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:36.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:36.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:36.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:36.611][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:36.972][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:36.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-17 21:07:36.987][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-17 21:07:36.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:36.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:36.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.062][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:37.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-17 21:07:37.098][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:37.099][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-17 21:07:37.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.114][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.117][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:37.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-17 21:07:37.120][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:37.121][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-17 21:07:37.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.146][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.150][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:37.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-17 21:07:37.153][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:37.154][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-17 21:07:37.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.165][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.DEBUG[2025-03-17 21:07:37.167][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:37.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-17 21:07:37.172][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:37.174][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-17 21:07:37.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:37.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:37.191][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:37.193][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:37.560][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:37.925][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:37.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-17 21:07:37.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-17 21:07:37.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:37.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:37.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:37.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:37.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:37.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:37.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-17 21:07:37.951][biodb::testThat]
biodb.INFO [2025-03-17 21:07:37.952][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-17 21:07:37.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:37.954][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:37.957][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:37.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:37.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:37.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:38.324][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:38.681][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:38.685][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-17 21:07:38.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-17 21:07:38.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:38.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:38.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:38.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:38.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:38.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:38.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:38.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:38.730][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:38.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:38.735][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:39.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:39.486][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:39.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-17 21:07:39.504][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-17 21:07:39.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:39.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:39.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:39.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:39.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:39.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-17 21:07:39.550][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-17 21:07:39.553][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-17 21:07:39.555][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-17 21:07:39.557][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-17 21:07:39.559][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:39.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:39.562][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:39.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:39.565][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-17 21:07:39.573][biodb::testContext]
biodb.INFO [2025-03-17 21:07:39.574][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:39.576][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-17 21:07:39.577][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:39.579][biodb::testContext]
biodb.INFO [2025-03-17 21:07:39.582][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:39.585][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:39.591][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:39.593][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-17 21:07:39.595][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.600][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-17 21:07:39.602][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.607][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-17 21:07:39.608][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.612][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-17 21:07:39.613][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-17 21:07:39.614][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-17 21:07:39.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.617][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-17 21:07:39.618][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-17 21:07:39.619][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.623][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-17 21:07:39.624][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-17 21:07:39.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.628][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-17 21:07:39.629][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-17 21:07:39.630][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-17 21:07:39.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.634][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-17 21:07:39.635][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.638][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-17 21:07:39.639][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-17 21:07:39.641][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-17 21:07:39.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.644][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:39.645][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-17 21:07:39.646][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-17 21:07:39.647][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-17 21:07:39.648][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-17 21:07:39.649][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-17 21:07:39.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.653][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-17 21:07:39.654][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-17 21:07:39.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.658][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-17 21:07:39.659][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-17 21:07:39.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.663][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-17 21:07:39.664][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-17 21:07:39.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.667][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-17 21:07:39.668][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-17 21:07:39.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.672][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-17 21:07:39.673][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-17 21:07:39.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.677][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:39.678][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-17 21:07:39.681][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-17 21:07:39.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.685][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-17 21:07:39.686][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-17 21:07:39.687][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-17 21:07:39.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:39.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:39.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:39.691][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-17 21:07:39.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:39.694][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-17 21:07:39.695][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.696][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:39.697][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.698][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:39.699][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:39.700][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:39.701][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:39.702][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:39.703][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.704][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-17 21:07:39.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:39.706][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:39.707][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.709][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:39.709][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:39.709][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:39.709][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:39.709][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:39.710][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:39.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:39.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:39.713][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:39.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:39.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:39.716][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:39.978][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:39.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:39.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:39.981][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:39.982][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:39.983][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-17 21:07:39.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:39.986][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:39.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:39.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.989][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:39.990][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:39.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:39.992][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:39.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:39.994][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.995][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-17 21:07:39.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:39.997][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:39.998][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:39.999][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:39.999][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:39.999][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:39.999][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:39.999][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:40.000][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:40.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:40.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.006][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:40.008][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:40.009][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.010][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.011][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-17 21:07:40.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.014][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-17 21:07:40.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:40.017][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.021][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:40.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:40.023][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.023][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-17 21:07:40.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:40.025][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.027][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:40.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:40.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.034][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:40.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:40.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.038][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.039][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-17 21:07:40.041][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.042][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:40.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:40.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.046][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.048][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:40.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:40.050][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.051][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-17 21:07:40.052][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:40.053][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.054][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.055][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.056][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:40.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:40.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.062][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.063][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:40.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:40.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.066][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:40.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:40.068][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.094][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[2025-03-17 21:07:40.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.138][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[2025-03-17 21:07:40.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.143][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-17 21:07:40.144][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-17 21:07:40.146][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-17 21:07:40.147][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-17 21:07:40.149][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:40.150][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-17 21:07:40.151][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:40.153][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:40.154][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-17 21:07:40.156][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-17 21:07:40.157][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:40.159][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-17 21:07:40.160][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:40.162][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:40.163][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-17 21:07:40.164][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-17 21:07:40.166][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-17 21:07:40.167][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-17 21:07:40.169][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:40.170][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-17 21:07:40.171][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-17 21:07:40.173][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-17 21:07:40.174][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-17 21:07:40.176][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-17 21:07:40.177][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-17 21:07:40.179][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-17 21:07:40.180][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-17 21:07:40.182][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-17 21:07:40.183][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-17 21:07:40.185][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-17 21:07:40.186][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-17 21:07:40.188][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-17 21:07:40.189][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-17 21:07:40.191][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-17 21:07:40.193][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-17 21:07:40.194][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-17 21:07:40.196][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-17 21:07:40.197][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-17 21:07:40.199][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-17 21:07:40.201][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-17 21:07:40.203][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-17 21:07:40.204][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-17 21:07:40.206][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-17 21:07:40.207][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-17 21:07:40.209][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-17 21:07:40.211][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-17 21:07:40.212][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-17 21:07:40.214][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-17 21:07:40.216][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-17 21:07:40.217][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-17 21:07:40.219][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-17 21:07:40.220][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-17 21:07:40.222][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-17 21:07:40.224][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-17 21:07:40.225][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-17 21:07:40.227][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-17 21:07:40.228][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-17 21:07:40.230][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-17 21:07:40.231][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-17 21:07:40.233][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-17 21:07:40.234][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-17 21:07:40.236][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-17 21:07:40.238][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-17 21:07:40.239][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-17 21:07:40.241][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-17 21:07:40.242][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-17 21:07:40.244][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:40.246][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:40.247][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-17 21:07:40.249][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-17 21:07:40.250][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-17 21:07:40.252][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-17 21:07:40.253][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-17 21:07:40.255][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-17 21:07:40.256][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-17 21:07:40.258][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-17 21:07:40.260][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-17 21:07:40.261][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-17 21:07:40.263][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-17 21:07:40.264][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-17 21:07:40.266][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-17 21:07:40.267][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-17 21:07:40.269][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-17 21:07:40.271][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-17 21:07:40.272][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:40.273][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:40.274][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.276][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.316][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[2025-03-17 21:07:40.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.334][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[2025-03-17 21:07:40.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.357][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[2025-03-17 21:07:40.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.363][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[2025-03-17 21:07:40.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.369][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[2025-03-17 21:07:40.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:40.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:40.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:40.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:40.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:40.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:40.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:40.388][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:40.390][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-17 21:07:40.392][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.393][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.395][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:40.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.398][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.399][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-17 21:07:40.399][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-17 21:07:40.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:40.401][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.402][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-17 21:07:40.403][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-17 21:07:40.404][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-17 21:07:40.405][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:40.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:40.406][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:40.406][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:40.407][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-17 21:07:40.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:40.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:40.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:40.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:40.414][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:40.414][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-17 21:07:40.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:40.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:40.417][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:40.418][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-17 21:07:40.418][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-17 21:07:40.419][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:40.421][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:40.423][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-17 21:07:40.424][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:40.426][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:40.427][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:40.431][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-17 21:07:40.432][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-17 21:07:40.433][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-17 21:07:40.434][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-17 21:07:40.436][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:40.437][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:40.438][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-17 21:07:40.439][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-17 21:07:40.440][biodb::testThat]
biodb.INFO [2025-03-17 21:07:40.441][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-17 21:07:40.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:40.443][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:40.447][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-17 21:07:40.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:40.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-17 21:07:40.453][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:40.454][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-17 21:07:40.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:40.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:40.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:40.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-17 21:07:40.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-17 21:07:41.187][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:41.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-17 21:07:41.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-17 21:07:41.210][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-17 21:07:41.213][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-17 21:07:41.215][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-17 21:07:41.216][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-17 21:07:41.218][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.220][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.223][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-17 21:07:41.231][biodb::testContext]
biodb.INFO [2025-03-17 21:07:41.232][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:41.234][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-17 21:07:41.235][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-17 21:07:41.236][biodb::testContext]
biodb.INFO [2025-03-17 21:07:41.240][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:41.242][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:41.247][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:41.248][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-17 21:07:41.250][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.254][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-17 21:07:41.255][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.260][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-17 21:07:41.261][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.264][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-17 21:07:41.266][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-17 21:07:41.267][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-17 21:07:41.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.270][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-17 21:07:41.271][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-17 21:07:41.272][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.276][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-17 21:07:41.277][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-17 21:07:41.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.281][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-17 21:07:41.282][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-17 21:07:41.283][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-17 21:07:41.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.287][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-17 21:07:41.288][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.291][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-17 21:07:41.292][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-17 21:07:41.293][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-17 21:07:41.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.297][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:41.298][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-17 21:07:41.299][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-17 21:07:41.300][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-17 21:07:41.301][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-17 21:07:41.302][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-17 21:07:41.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.306][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-17 21:07:41.307][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-17 21:07:41.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.310][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-17 21:07:41.311][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-17 21:07:41.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.315][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-17 21:07:41.316][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-17 21:07:41.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.320][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-17 21:07:41.321][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-17 21:07:41.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.325][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-17 21:07:41.326][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-17 21:07:41.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.330][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-17 21:07:41.331][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-17 21:07:41.335][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-17 21:07:41.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.339][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-17 21:07:41.340][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-17 21:07:41.341][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-17 21:07:41.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.345][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-17 21:07:41.347][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.360][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-17 21:07:41.361][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:41.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.364][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.365][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.367][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:41.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:41.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.370][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-17 21:07:41.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:41.372][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:41.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:41.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:41.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:41.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:41.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:41.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:41.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.400][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.401][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:41.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:41.406][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.407][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.409][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-17 21:07:41.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.415][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:41.416][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:41.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.424][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:41.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:41.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.428][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-17 21:07:41.429][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:41.431][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.433][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:41.433][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:41.433][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:41.433][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-17 21:07:41.433][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-17 21:07:41.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:41.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.439][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:41.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.443][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.444][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.446][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:41.447][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:41.448][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.449][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.451][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-17 21:07:41.454][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.455][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-17 21:07:41.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.458][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:41.459][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.460][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.464][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-17 21:07:41.466][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:41.467][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.468][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-17 21:07:41.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:41.471][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.473][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.474][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.475][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:41.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:41.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.484][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.486][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:41.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:41.488][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.490][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.491][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-17 21:07:41.494][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.495][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-17 21:07:41.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.498][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:41.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.504][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.505][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-17 21:07:41.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:41.508][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.509][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-17 21:07:41.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:41.512][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.513][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.515][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.516][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-17 21:07:41.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:41.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.525][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:41.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:41.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.530][self$setPropertyValue]
biodb.DEBUG[2025-03-17 21:07:41.533][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:41.534][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.535][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[2025-03-17 21:07:41.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.573][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[2025-03-17 21:07:41.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.585][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[2025-03-17 21:07:41.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.591][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[2025-03-17 21:07:41.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.615][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[2025-03-17 21:07:41.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.632][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[2025-03-17 21:07:41.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.644][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-17 21:07:41.646][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-17 21:07:41.648][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-17 21:07:41.650][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-17 21:07:41.653][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:41.654][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-17 21:07:41.657][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:41.658][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:41.661][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-17 21:07:41.663][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-17 21:07:41.665][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:41.666][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-17 21:07:41.668][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-17 21:07:41.670][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-17 21:07:41.672][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-17 21:07:41.674][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-17 21:07:41.675][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-17 21:07:41.677][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-17 21:07:41.679][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:41.681][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-17 21:07:41.682][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-17 21:07:41.684][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-17 21:07:41.686][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-17 21:07:41.688][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-17 21:07:41.690][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-17 21:07:41.692][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-17 21:07:41.693][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-17 21:07:41.695][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-17 21:07:41.697][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-17 21:07:41.699][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-17 21:07:41.701][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-17 21:07:41.702][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-17 21:07:41.704][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-17 21:07:41.706][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-17 21:07:41.708][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-17 21:07:41.709][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-17 21:07:41.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-17 21:07:41.713][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-17 21:07:41.715][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-17 21:07:41.717][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-17 21:07:41.718][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-17 21:07:41.720][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-17 21:07:41.722][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-17 21:07:41.724][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-17 21:07:41.725][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-17 21:07:41.727][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-17 21:07:41.729][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-17 21:07:41.731][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-17 21:07:41.733][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-17 21:07:41.734][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-17 21:07:41.736][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-17 21:07:41.738][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-17 21:07:41.740][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-17 21:07:41.741][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-17 21:07:41.743][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-17 21:07:41.745][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-17 21:07:41.747][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-17 21:07:41.748][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-17 21:07:41.750][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-17 21:07:41.752][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-17 21:07:41.754][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-17 21:07:41.756][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-17 21:07:41.757][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-17 21:07:41.759][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-17 21:07:41.761][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-17 21:07:41.763][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-17 21:07:41.765][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:41.766][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:41.767][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-17 21:07:41.769][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-17 21:07:41.770][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-17 21:07:41.772][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-17 21:07:41.774][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-17 21:07:41.775][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-17 21:07:41.777][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-17 21:07:41.805][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-17 21:07:41.807][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-17 21:07:41.809][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-17 21:07:41.811][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-17 21:07:41.812][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-17 21:07:41.814][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-17 21:07:41.816][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-17 21:07:41.817][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-17 21:07:41.819][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-17 21:07:41.821][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-17 21:07:41.822][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-17 21:07:41.823][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.826][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.865][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[2025-03-17 21:07:41.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.887][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[2025-03-17 21:07:41.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.892][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[2025-03-17 21:07:41.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.898][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[2025-03-17 21:07:41.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.903][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[2025-03-17 21:07:41.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.914][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[2025-03-17 21:07:41.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-17 21:07:41.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:41.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:41.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:41.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:41.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:41.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:41.921][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-17 21:07:41.923][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-17 21:07:41.924][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.925][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-17 21:07:41.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.930][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.931][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-17 21:07:41.932][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-17 21:07:41.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-17 21:07:41.934][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.934][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-17 21:07:41.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-17 21:07:41.936][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-17 21:07:41.937][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-17 21:07:41.938][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-17 21:07:41.938][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-17 21:07:41.938][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-17 21:07:41.939][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-17 21:07:41.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-17 21:07:41.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-17 21:07:41.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-17 21:07:41.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-17 21:07:41.945][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:41.945][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-17 21:07:41.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-17 21:07:41.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-17 21:07:41.948][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-17 21:07:41.949][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-17 21:07:41.949][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-17 21:07:41.950][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-17 21:07:41.952][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-17 21:07:41.953][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-17 21:07:41.954][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-17 21:07:41.956][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-17 21:07:41.957][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-17 21:07:41.961][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-17 21:07:41.962][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-17 21:07:41.963][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-17 21:07:41.965][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-17 21:07:41.966][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:41.967][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-17 21:07:41.968][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-17 21:07:41.969][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-17 21:07:41.974][biodb::testThat]
biodb.INFO [2025-03-17 21:07:41.975][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-17 21:07:41.976][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-17 21:07:41.977][biodb::testThat]
biodb.DEBUG[2025-03-17 21:07:41.981][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-17 21:07:41.985][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:41.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-17 21:07:41.987][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:41.989][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-17 21:07:41.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-17 21:07:41.995][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-17 21:07:41.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-17 21:07:41.998][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-17 21:07:42.026][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-17 21:07:42.031][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-17 21:07:42.032][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-17 21:07:42.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-17 21:07:42.035][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-17 21:07:42.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-17 21:07:42.037][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-17 21:07:42.038][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-17 21:07:42.039][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-17 21:07:42.040][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-17 21:07:42.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:42.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:42.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:42.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:42.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:42.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:42.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-17 21:07:42.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-17 21:07:42.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-17 21:07:42.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-17 21:07:42.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-17 21:07:43.307][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-17 21:07:44.488][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-17 21:07:44.493][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-17 21:07:44.500][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-17 21:07:44.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-17 21:07:44.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-17 21:07:44.512][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-17 21:07:44.514][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-17 21:07:44.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-17 21:07:44.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:44.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:44.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:44.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:44.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:44.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-17 21:07:44.538][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.548][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:44.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:44.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-17 21:07:44.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-17 21:07:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.557][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:44.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:44.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-17 21:07:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-17 21:07:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.565][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-17 21:07:44.566][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-17 21:07:44.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-17 21:07:44.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-17 21:07:44.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.573][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:44.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:44.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.577][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:44.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-17 21:07:44.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.581][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:44.582][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:44.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-17 21:07:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-17 21:07:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.598][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:44.599][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:44.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:44.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-17 21:07:44.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.605][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:44.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:44.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-17 21:07:44.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-17 21:07:44.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.613][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:44.614][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:44.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.616][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-17 21:07:44.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-17 21:07:44.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.621][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:44.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:44.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-17 21:07:44.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-17 21:07:44.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-17 21:07:44.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-17 21:07:44.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-17 21:07:44.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-17 21:07:44.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-17 21:07:44.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-17 21:07:44.663][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-17 21:07:44.666][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-17 21:07:44.667][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-17 21:07:44.668][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-17 21:07:44.669][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-17 21:07:44.670][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-17 21:07:44.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-17 21:07:44.671][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-17 21:07:44.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-17 21:07:44.673][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-17 21:07:44.673][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 363 ]
>
> proc.time()
user system elapsed
18.267 1.122 35.299
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.954 | 0.079 | 1.911 | |
| ChebiEntry | 0.138 | 0.001 | 0.139 | |