Pierrick Roger
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:08 -0400 (Mon, 10 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" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2025-03-07 00:32:03 -0500 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 00:35:41 -0500 (Fri, 07 Mar 2025) |
| EllapsedTime: 218.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 4.685 1.209 7.479
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-07 00:33:31.845][biodb::testContext]
biodb.INFO [2025-03-07 00:33:31.852][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:33:31.855][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-07 00:33:31.857][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:33:31.860][biodb::testContext]
biodb.INFO [2025-03-07 00:33:31.874][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:33:31.878][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 00:33:31.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:33:31.896][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 00:33:31.899][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 00:33:31.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:31.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:31.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:31.909][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 00:33:31.980][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 00:33:31.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:31.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:31.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:31.987][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 00:33:31.989][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 00:33:31.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:31.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:31.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:31.996][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 00:33:31.999][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 00:33:32.001][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 00:33:32.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.007][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[2025-03-07 00:33:32.009][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 00:33:32.011][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 00:33:32.014][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 00:33:32.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.022][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 00:33:32.024][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 00:33:32.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.032][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 00:33:32.034][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 00:33:32.037][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 00:33:32.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.045][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 00:33:32.047][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 00:33:32.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.054][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[2025-03-07 00:33:32.056][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 00:33:32.058][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 00:33:32.060][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 00:33:32.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.069][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:33:32.071][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 00:33:32.073][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 00:33:32.076][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 00:33:32.078][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 00:33:32.080][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 00:33:32.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.086][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.DEBUG[2025-03-07 00:33:32.088][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 00:33:32.091][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 00:33:32.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.098][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 00:33:32.101][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 00:33:32.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.109][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 00:33:32.112][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 00:33:32.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.121][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 00:33:32.123][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 00:33:32.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.129][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[2025-03-07 00:33:32.132][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 00:33:32.134][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 00:33:32.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.143][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:33:32.146][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 00:33:32.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 00:33:32.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.175][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 00:33:32.178][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 00:33:32.181][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 00:33:32.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.194][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 00:33:32.279][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.321][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 00:33:32.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:33:32.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.330][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.337][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:33:32.340][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:33:32.342][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.344][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 00:33:32.346][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:33:32.349][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.353][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:33:32.353][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:33:32.353][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:33:32.353][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:33:32.353][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:33:32.355][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:33:32.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.362][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:33:32.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.377][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.379][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:33:32.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:33:32.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.387][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.390][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 00:33:32.394][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.397][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:33:32.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:33:32.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.412][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:33:32.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:33:32.416][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.418][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 00:33:32.421][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:33:32.423][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:33:32.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:33:32.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:33:32.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:33:32.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:33:32.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:33:32.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:33:32.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.443][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.445][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:33:32.447][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:33:32.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.452][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.455][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 00:33:32.459][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.461][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 00:33:32.464][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:33:32.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.473][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.477][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:33:32.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:33:32.482][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.484][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 00:33:32.486][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:33:32.488][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.492][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.495][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:33:32.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:33:32.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.508][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.511][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:33:32.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:33:32.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.519][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.522][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 00:33:32.526][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:33:32.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:33:32.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.539][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.541][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.543][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:33:32.546][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:33:32.548][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.551][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 00:33:32.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:33:32.555][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:32.560][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:33:32.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.568][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:33:32.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:32.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:32.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:33:32.577][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.580][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:33:32.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:33:32.584][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:32.587][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:33:32.593][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:33:32.596][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.662][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[2025-03-07 00:33:32.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:32.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:32.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:32.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:32.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:32.791][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 00:33:32.800][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 00:33:32.803][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 00:33:32.807][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 00:33:32.810][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:33:32.814][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 00:33:32.817][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 00:33:32.820][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 00:33:32.824][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 00:33:32.827][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 00:33:32.830][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:33:32.834][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 00:33:32.837][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 00:33:32.841][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 00:33:32.844][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 00:33:32.848][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 00:33:32.852][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 00:33:32.855][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 00:33:32.858][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:33:32.862][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 00:33:32.865][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 00:33:32.869][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 00:33:32.872][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 00:33:32.876][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 00:33:32.880][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 00:33:32.883][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 00:33:32.886][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 00:33:32.890][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 00:33:32.893][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 00:33:32.896][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 00:33:32.899][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 00:33:32.903][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 00:33:32.906][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 00:33:32.909][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 00:33:32.912][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 00:33:32.916][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 00:33:32.919][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 00:33:32.923][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 00:33:32.926][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 00:33:32.929][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 00:33:32.931][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 00:33:32.935][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 00:33:32.938][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 00:33:32.942][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 00:33:32.945][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 00:33:32.949][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 00:33:32.952][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 00:33:32.956][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 00:33:32.960][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 00:33:32.964][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 00:33:32.968][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 00:33:32.971][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 00:33:32.975][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 00:33:32.979][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 00:33:32.982][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 00:33:32.985][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 00:33:32.987][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 00:33:32.991][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 00:33:32.994][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 00:33:32.998][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 00:33:33.001][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 00:33:33.005][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 00:33:33.008][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 00:33:33.012][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 00:33:33.015][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 00:33:33.019][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 00:33:33.022][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:33:33.026][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:33:33.029][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 00:33:33.033][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 00:33:33.036][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 00:33:33.039][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 00:33:33.042][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 00:33:33.045][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 00:33:33.049][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 00:33:33.052][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 00:33:33.056][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 00:33:33.059][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 00:33:33.062][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 00:33:33.065][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 00:33:33.069][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 00:33:33.072][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 00:33:33.075][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 00:33:33.091][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 00:33:33.095][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:33:33.101][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:33:33.103][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.107][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.132][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[2025-03-07 00:33:33.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.269][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[2025-03-07 00:33:33.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.342][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[2025-03-07 00:33:33.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.357][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[2025-03-07 00:33:33.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:33:33.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:33.376][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 00:33:33.403][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 00:33:33.408][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:33.410][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 00:33:33.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:33.415][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:33:33.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:33.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:33:33.422][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:33.425][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 00:33:33.427][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 00:33:33.429][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:33:33.431][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:33.433][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 00:33:33.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 00:33:33.438][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 00:33:33.441][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 00:33:33.443][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:33:33.443][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:33:33.443][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:33:33.445][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 00:33:33.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:33.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:33.452][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:33:33.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:33:33.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:33:33.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:33:33.460][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:33.460][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 00:33:33.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:33:33.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:33:33.467][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 00:33:33.469][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 00:33:33.469][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 00:33:33.485][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:33:33.488][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:33:33.492][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 00:33:33.495][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:33:33.499][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:33:33.503][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:33:33.545][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 00:33:33.548][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 00:33:33.555][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 00:33:33.563][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 00:33:33.571][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:33:33.574][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:33:33.577][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 00:33:33.579][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 00:33:33.598][biodb::testThat]
biodb.INFO [2025-03-07 00:33:33.600][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-07 00:33:33.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:33.605][biodb::testThat]
biodb.TRACE[2025-03-07 00:33:33.613][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-07 00:33:33.628][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:33.634][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:33.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:33.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:33.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:33.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:33.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:33.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:33.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:33.702][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:33.704][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:33.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.754][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:33.757][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:33.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.839][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:33.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.849][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:33.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:33.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:33.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.868][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:33.870][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:33.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:33.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:33.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:33.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:33.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.912][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:33.915][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:33.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.932][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:33.934][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:33.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.941][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:33.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:33.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:33.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:33.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:33.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.973][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:33.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:33.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:33.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:33.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:33.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:33.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:34.041][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:34.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.049][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:34.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.058][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:34.061][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:34.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.068][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:34.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:34.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:34.257][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-07 00:33:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:34.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:34.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:34.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:34.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:34.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:34.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:34.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:34.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:34.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.387][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:34.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:34.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.396][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:34.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:34.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.404][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:34.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:34.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.750][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.753][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:34.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.830][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.834][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:34.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:34.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:34.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:34.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:34.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.891][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:34.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:34.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:34.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:34.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.936][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:34.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.955][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:34.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:34.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.022][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.120][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.138][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.157][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.166][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.206][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.215][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.225][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.228][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.236][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.263][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.272][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.282][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.292][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.294][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.341][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.361][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.370][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.432][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.512][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.548][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:35.550][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:35.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.566][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:35.568][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:35.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.581][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:35.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:35.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.598][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:35.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:35.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.615][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.617][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:35.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.634][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.636][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:35.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.653][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.655][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:35.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.672][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.675][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:35.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.691][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.693][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:35.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:35.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:35.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:35.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:35.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.736][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 00:33:35.755][biodb::testThat]
biodb.INFO [2025-03-07 00:33:35.757][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-07 00:33:35.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:35.762][biodb::testThat]
biodb.DEBUG[2025-03-07 00:33:35.799][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-07 00:33:35.811][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:35.819][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-07 00:33:35.822][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:35.826][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-07 00:33:35.828][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:35.901][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:35.904][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:35.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:35.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:35.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:35.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:35.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:35.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:35.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:35.935][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:35.939][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:35.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:35.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:35.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:35.999][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:36.002][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:36.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.008][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:36.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.016][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:36.019][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:36.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:36.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:36.036][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:36.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:36.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.052][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:36.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:36.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:36.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:36.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.078][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:36.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:36.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.087][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:36.090][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:36.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.097][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:36.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.106][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:36.108][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:36.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:36.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.125][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.127][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:36.175][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:36.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.182][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:36.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:36.195][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:36.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:36.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:36.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:36.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:36.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:36.305][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-07 00:33:36.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-07 00:33:36.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-07 00:33:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-07 00:33:36.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-07 00:33:36.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-07 00:33:36.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-07 00:33:36.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:33:36.350][biodb::testThat]
biodb.INFO [2025-03-07 00:33:36.352][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-07 00:33:36.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:36.356][biodb::testThat]
biodb.TRACE[2025-03-07 00:33:36.362][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.369][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:36.372][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-07 00:33:36.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:36.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:36.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:36.474][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-07 00:33:36.482][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 00:33:36.518][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:33:36.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 00:33:36.562][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:36.565][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 00:33:36.625][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[2025-03-07 00:33:36.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:36.635][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:36.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:33:37.552][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:33:38.145][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:38.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-07 00:33:38.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-07 00:33:38.191][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-07 00:33:38.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:38.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:38.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.227][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.230][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.250][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 00:33:38.260][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.262][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-07 00:33:38.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:38.267][biodb::testThat]
biodb.TRACE[2025-03-07 00:33:38.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:38.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:38.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:38.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:38.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:38.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:38.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:38.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:33:38.537][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:33:38.540][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:33:38.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:38.546][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-07 00:33:38.584][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.586][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-07 00:33:38.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:38.590][biodb::testThat]
biodb.TRACE[2025-03-07 00:33:38.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:38.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:38.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:38.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:38.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.699][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:38.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:38.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:38.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:38.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:38.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:38.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:38.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:38.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:38.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.840][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 00:33:38.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:38.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 00:33:38.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 00:33:38.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:38.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:33:38.895][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.897][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-07 00:33:38.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:38.902][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.920][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.923][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-07 00:33:38.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:38.927][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.947][biodb::testThat]
biodb.INFO [2025-03-07 00:33:38.949][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-07 00:33:38.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:38.954][biodb::testThat]
biodb.DEBUG[2025-03-07 00:33:38.963][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-07 00:33:39.609][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-07 00:33:40.510][biodb::testThat]
biodb.INFO [2025-03-07 00:33:40.521][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-07 00:33:40.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:40.532][biodb::testThat]
biodb.DEBUG[2025-03-07 00:33:40.984][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[2025-03-07 00:33:41.425][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:41.428][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:41.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.432][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.435][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:41.437][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:41.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.442][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 00:33:41.445][biodb::testThat]
biodb.INFO [2025-03-07 00:33:41.448][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-07 00:33:41.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:33:41.452][biodb::testThat]
biodb.TRACE[2025-03-07 00:33:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:41.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:41.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:41.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:41.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:41.695][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:33:41.702][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:33:41.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:33:41.708][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:41.710][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 00:33:41.870][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:33:41.877][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:33:41.880][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:33:41.883][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:41.886][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-07 00:33:41.914][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 00:33:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 00:33:41.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:41.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:41.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:41.996][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:33:42.039][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:42.042][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:42.090][private$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[2025-03-07 00:33:42.498][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[2025-03-07 00:33:42.906][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:42.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-07 00:33:42.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-07 00:33:42.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:42.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:42.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:42.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:42.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:42.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:42.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:42.998][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-07 00:33:43.143][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:43.147][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-07 00:33:43.150][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:43.153][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:43.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:43.157][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:43.159][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:43.161][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:43.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:43.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:43.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:43.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:43.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:43.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:43.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:43.192][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-07 00:33:43.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:43.202][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:43.205][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-07 00:33:43.966][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-07 00:33:44.380][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:44.385][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-07 00:33:44.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-07 00:33:44.400][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-07 00:33:44.404][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:44.407][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:44.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:44.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:44.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:44.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:44.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:44.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:44.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:44.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:44.443][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.450][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.463][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:44.465][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:44.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.473][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:44.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:44.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.482][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:44.484][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:44.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:44.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:44.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.500][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:44.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:44.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:44.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.520][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:44.522][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:44.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:44.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.554][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:44.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:44.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.564][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:44.567][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:44.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:44.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:44.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.603][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:44.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:44.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:44.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:44.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.624][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:44.626][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:44.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:44.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:44.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.645][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:44.648][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:44.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:44.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:44.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:44.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:44.764][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-07 00:33:44.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:44.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:44.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:44.819][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[2025-03-07 00:33:44.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:44.829][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:44.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:33:45.233][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:33:45.637][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:45.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-07 00:33:45.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-07 00:33:45.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:45.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:45.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:45.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:45.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:45.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:45.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:45.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:45.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:45.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:45.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:45.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:45.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:45.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:45.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:45.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:45.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:45.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:45.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:45.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:45.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:45.776][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-07 00:33:45.778][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:45.781][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-07 00:33:45.784][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:45.786][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:45.788][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:45.790][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:45.792][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:45.794][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:45.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:45.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:45.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:45.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:45.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:45.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:45.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:45.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-07 00:33:45.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:45.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:45.864][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-07 00:33:46.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-07 00:33:46.793][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:46.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-07 00:33:46.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-07 00:33:46.823][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-07 00:33:46.828][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:46.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:46.835][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:46.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:46.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:46.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:46.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:46.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:46.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:46.863][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[2025-03-07 00:33:46.867][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:46.870][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:46.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:46.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:46.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.885][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:46.890][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:46.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.898][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:46.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.906][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:46.909][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:46.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.928][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:46.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:46.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:46.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:46.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:46.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:46.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.979][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:46.982][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:46.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.987][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:46.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:46.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:46.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:46.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.002][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:47.005][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:47.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.013][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:47.015][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:47.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:47.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:47.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:47.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.055][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:47.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:47.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:47.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:47.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.078][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:47.081][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:47.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.089][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:47.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:47.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.098][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:47.100][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:47.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.108][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:47.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:47.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:47.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:47.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:47.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:47.278][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-07 00:33:47.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:47.381][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:33:47.389][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:33:47.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:33:47.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:33:47.399][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 00:33:47.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:47.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:47.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:47.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:47.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:47.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:47.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:47.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:47.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:47.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:47.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:47.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:47.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:47.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:47.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:47.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:47.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:47.515][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-07 00:33:47.517][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:47.528][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-07 00:33:47.532][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:47.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:47.538][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:47.540][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:47.543][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:47.546][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:47.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:47.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:47.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:47.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:47.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:47.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:47.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:47.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-07 00:33:47.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:47.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:47.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-07 00:33:48.060][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-07 00:33:48.466][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:48.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-07 00:33:48.478][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-07 00:33:48.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-07 00:33:48.484][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:48.487][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:48.489][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:48.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:48.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:48.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:48.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:48.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:48.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:48.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:48.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.534][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:48.537][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:48.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.544][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:48.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:48.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:48.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:48.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.563][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:48.565][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:48.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:48.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:48.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.581][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:48.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.589][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:48.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:48.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.598][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:48.600][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:48.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.628][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:48.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:48.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.637][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:48.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.646][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:48.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:48.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:48.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:48.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:48.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:48.744][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-07 00:33:48.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:48.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:48.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:48.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:48.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:48.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:48.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:48.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:48.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:48.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:48.837][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-07 00:33:48.848][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:48.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-07 00:33:48.855][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:48.858][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:48.861][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:48.863][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:48.866][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:48.868][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:48.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:48.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:48.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:48.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:48.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:48.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:48.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:48.899][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-07 00:33:48.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:48.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:48.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-07 00:33:49.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-07 00:33:49.852][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:49.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-07 00:33:49.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-07 00:33:49.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-07 00:33:49.876][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:49.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:49.882][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:49.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:49.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:49.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:49.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:49.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:49.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:49.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:49.912][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:49.915][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:49.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:49.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.932][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:49.934][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:49.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.942][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:49.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:49.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.953][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:49.956][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:49.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.960][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.963][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:49.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:49.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.972][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:49.975][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:49.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.978][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.980][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:49.982][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:49.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.988][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:49.990][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:49.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:49.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:49.998][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:50.014][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:50.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:50.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.032][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:50.035][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:50.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:50.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:50.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.053][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:50.056][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:50.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:50.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:50.154][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-07 00:33:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:50.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:50.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:50.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:50.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:50.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:50.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:50.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:50.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:50.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:50.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:50.226][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-07 00:33:50.228][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:50.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-07 00:33:50.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:50.237][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:50.239][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:50.241][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:50.244][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:50.246][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:50.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:50.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:50.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:50.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:50.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:50.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:50.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:50.276][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-07 00:33:50.282][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:50.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:50.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-07 00:33:50.818][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-07 00:33:51.221][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:51.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-07 00:33:51.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-07 00:33:51.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-07 00:33:51.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:51.245][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:51.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:51.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:51.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:51.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:51.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:51.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:51.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:51.279][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.299][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:51.301][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:51.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.309][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:51.311][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:51.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:51.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:51.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:51.332][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:51.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:51.343][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:51.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.347][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.349][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:51.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.359][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:51.361][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:51.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.379][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:51.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:51.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:51.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:51.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.398][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:51.400][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:51.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.407][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:51.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:51.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.415][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:51.418][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:51.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:51.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:51.517][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-07 00:33:51.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:51.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:51.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:51.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:51.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:51.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:51.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:51.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:51.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:51.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:51.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:51.596][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-07 00:33:51.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:51.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-07 00:33:51.605][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:51.607][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:51.610][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:51.612][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:51.615][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:51.617][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:51.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:51.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:51.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:51.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:51.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:51.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:51.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:51.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-07 00:33:51.653][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:51.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:51.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-07 00:33:52.176][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-07 00:33:52.634][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:52.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-07 00:33:52.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-07 00:33:52.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-07 00:33:52.655][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:52.658][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:52.661][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:52.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:52.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:52.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:52.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:52.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:52.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:52.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:52.687][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.703][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:52.706][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:52.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:52.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.721][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:52.723][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:52.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.738][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:52.740][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:52.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:52.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.768][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:52.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:52.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:52.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:52.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.781][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:52.784][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:52.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.791][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:52.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.800][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:52.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:52.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.810][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.819][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:52.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:52.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:52.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.836][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:52.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:52.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:52.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:52.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:52.858][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:52.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.865][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:52.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:52.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.872][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:52.873][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:52.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:52.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:52.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:52.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:52.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:52.985][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-07 00:33:52.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:52.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:52.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:52.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:53.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:53.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:53.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:53.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:53.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:53.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:53.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:53.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:53.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:53.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:53.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:53.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:53.039][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-07 00:33:53.041][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:53.045][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-07 00:33:53.047][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:53.049][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:53.051][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:53.054][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:53.056][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:53.058][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:53.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:53.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:53.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:53.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:53.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:53.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:53.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:53.088][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-07 00:33:53.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:53.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:53.098][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-07 00:33:53.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-07 00:33:54.013][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:54.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-07 00:33:54.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-07 00:33:54.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-07 00:33:54.037][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:54.039][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:54.044][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:54.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:54.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:54.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:54.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:54.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:54.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:54.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:54.076][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.079][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.110][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:54.113][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:54.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.120][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.129][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:54.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:54.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:54.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.147][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:54.149][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:54.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:54.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.166][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:54.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:54.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:54.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:54.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:54.187][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:54.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.194][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:54.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.204][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:54.206][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.213][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.221][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:54.223][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:54.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:54.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.239][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:54.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:54.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:54.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.257][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:54.259][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:54.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.266][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:54.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:54.278][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:54.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.286][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:54.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:54.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:54.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:54.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:54.394][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-07 00:33:54.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:54.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:54.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:54.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:54.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:54.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:54.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:54.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:54.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:54.447][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-07 00:33:54.449][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:54.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-07 00:33:54.456][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:54.458][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:54.460][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:54.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:54.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:54.467][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:54.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:54.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:54.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:54.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:54.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:54.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:54.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:54.495][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-07 00:33:54.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:54.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:54.508][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-07 00:33:54.981][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-07 00:33:55.408][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:55.412][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-07 00:33:55.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-07 00:33:55.426][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-07 00:33:55.430][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:55.433][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:55.436][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:55.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:55.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:55.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:55.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:55.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:55.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:55.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:55.466][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.487][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:55.490][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:55.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.498][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.509][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:55.511][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:55.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:55.532][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:55.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:55.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:55.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:55.553][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:55.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:55.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:55.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.573][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:55.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:55.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.584][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:55.587][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.592][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.595][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:55.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:55.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:55.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.628][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:55.630][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:55.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.662][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:55.664][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:55.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:55.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.682][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:55.685][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:55.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.692][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:55.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:55.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:55.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:55.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:55.809][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-07 00:33:55.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:55.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:55.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:55.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:55.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:55.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:55.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:55.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:55.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:55.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:55.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:55.878][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-07 00:33:55.881][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:55.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-07 00:33:55.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:55.902][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:55.904][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:55.908][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:55.911][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:55.913][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:55.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:55.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:55.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:55.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:55.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:55.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:55.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:55.951][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-07 00:33:55.958][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:55.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:55.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-07 00:33:56.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-07 00:33:56.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:56.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-07 00:33:56.840][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-07 00:33:56.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-07 00:33:56.850][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:56.853][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:56.856][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:56.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:56.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:56.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:56.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:56.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:56.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:56.882][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[2025-03-07 00:33:56.888][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:56.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:56.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:56.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:56.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.908][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:56.911][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:56.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.919][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:56.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.929][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:56.931][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:56.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.936][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.939][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:56.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.949][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:56.952][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:56.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:56.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:56.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.965][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:56.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:56.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.972][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:56.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:56.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:56.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:56.996][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:56.998][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:57.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.006][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:57.008][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.015][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:57.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:57.028][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:57.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:57.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.045][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:57.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:57.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:57.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:57.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.066][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:57.068][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:57.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:57.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:57.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:57.087][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:57.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:57.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:57.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:57.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:57.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:57.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:57.215][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-07 00:33:57.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:57.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:57.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:57.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:57.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:57.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:57.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:57.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:57.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:57.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:57.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:57.297][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-07 00:33:57.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:57.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-07 00:33:57.310][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:57.312][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:57.318][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:57.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:57.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:57.325][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:57.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:57.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:57.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:57.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:57.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:57.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:57.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:57.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-07 00:33:57.365][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:57.368][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:57.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-07 00:33:57.810][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-07 00:33:58.227][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:58.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-07 00:33:58.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-07 00:33:58.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-07 00:33:58.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:58.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:58.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:58.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:58.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:58.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:58.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:58.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:58.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:58.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:58.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.308][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:58.311][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:58.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.318][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:58.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.335][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:58.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:58.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:58.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:58.362][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:58.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:58.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:58.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.380][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:58.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:58.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:58.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.399][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:58.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:58.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.408][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:58.411][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.418][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:58.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.428][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:58.430][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:58.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:58.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.447][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:58.449][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:58.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:58.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.466][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:58.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:58.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.476][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:58.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:58.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.486][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:58.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:58.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:58.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:58.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:58.616][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-07 00:33:58.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:58.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:58.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:33:58.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:58.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:58.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:58.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:58.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:58.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:58.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:58.675][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-07 00:33:58.678][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:33:58.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-07 00:33:58.684][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:33:58.687][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:33:58.690][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:33:58.692][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:33:58.695][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:33:58.699][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:33:58.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:58.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:58.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:58.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:58.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:58.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:58.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:33:58.734][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-07 00:33:58.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:33:58.744][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:33:58.747][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-07 00:33:59.214][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-07 00:33:59.629][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:33:59.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-07 00:33:59.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-07 00:33:59.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-07 00:33:59.652][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:33:59.655][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:33:59.658][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:33:59.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:33:59.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:33:59.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:33:59.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:33:59.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:33:59.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:33:59.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:33:59.703][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:59.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:59.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:59.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:59.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.724][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:59.726][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:59.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:33:59.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:33:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.744][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:59.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:59.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:33:59.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:33:59.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.765][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:59.768][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:59.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:33:59.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:33:59.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.787][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:59.789][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:59.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.794][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:33:59.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:33:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.807][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:59.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:33:59.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.815][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.818][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:59.821][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:59.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.829][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:33:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:33:59.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:59.843][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:59.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:59.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:33:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.861][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:59.863][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:59.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:33:59.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:33:59.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.881][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:59.884][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:59.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:33:59.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:33:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.904][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:59.907][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:59.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.927][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:33:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:33:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:59.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:59.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:33:59.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:59.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:33:59.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:33:59.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:33:59.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:33:59.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:00.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:00.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:00.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:00.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:00.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:00.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:00.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:00.038][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-07 00:34:00.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:00.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:00.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:00.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:00.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:00.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:00.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:00.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:00.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:00.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:00.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:00.100][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-07 00:34:00.103][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:00.107][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-07 00:34:00.110][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:00.113][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:00.117][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:00.120][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:00.122][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:00.126][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:00.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:00.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:00.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:00.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:00.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:00.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:00.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:00.168][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-07 00:34:00.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:00.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:00.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-07 00:34:00.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-07 00:34:01.028][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:01.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-07 00:34:01.041][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-07 00:34:01.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-07 00:34:01.052][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:01.054][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:01.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:01.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:01.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:01.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:01.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:01.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:01.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:01.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:01.089][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.109][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:01.112][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:01.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:01.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:01.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.130][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:01.133][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:01.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.137][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:01.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.150][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:01.153][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:01.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:01.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:01.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.170][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:01.173][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:01.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:01.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.191][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:01.194][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:01.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.203][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:01.206][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.214][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:01.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.225][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:01.228][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:01.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:01.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.448][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:01.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:01.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:01.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:01.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:01.471][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:01.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.491][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:01.495][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:01.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:01.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:01.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:01.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:01.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:01.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:01.610][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-07 00:34:01.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:01.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:01.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:01.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:01.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:01.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:01.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:01.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:01.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:01.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:01.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:01.669][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-07 00:34:01.671][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:01.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-07 00:34:01.678][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:01.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:01.684][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:01.687][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:01.689][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:01.692][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:01.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:01.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:01.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:01.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:01.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:01.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:01.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:01.727][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-07 00:34:01.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:01.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:01.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-07 00:34:02.151][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-07 00:34:02.547][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:02.552][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-07 00:34:02.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-07 00:34:02.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-07 00:34:02.574][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:02.577][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:02.580][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:02.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:02.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:02.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:02.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:02.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:02.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:02.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:02.617][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.621][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.642][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:02.645][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:02.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.653][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:02.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:02.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.664][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:02.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:02.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.673][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.676][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:02.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.688][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:02.691][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:02.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.697][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:02.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:02.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.712][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:02.715][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:02.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.724][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:02.728][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.733][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:02.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.748][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:02.751][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:02.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.772][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:02.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:02.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:02.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:02.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.798][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:02.801][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:02.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.810][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:02.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:02.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.822][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:02.825][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:02.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:02.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:02.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:02.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:02.954][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-07 00:34:02.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:02.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:02.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:02.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:02.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:02.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:02.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:03.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:03.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:03.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:03.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:03.022][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-07 00:34:03.025][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:03.029][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-07 00:34:03.033][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:03.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:03.040][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:03.043][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:03.046][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:03.048][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:03.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:03.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:03.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:03.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:03.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:03.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:03.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:03.085][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-07 00:34:03.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:03.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:03.100][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-07 00:34:03.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-07 00:34:03.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:03.929][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-07 00:34:03.939][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-07 00:34:03.947][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-07 00:34:03.951][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:03.955][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:03.958][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:03.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:03.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:03.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:03.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:03.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:03.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:03.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:03.993][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:03.996][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:03.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.017][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:04.020][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:04.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.026][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.078][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:04.080][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:04.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.096][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:04.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:04.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:04.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.134][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:04.137][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:04.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.141][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.154][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:04.156][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:04.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.163][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:04.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.182][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:04.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:04.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:04.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.217][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:04.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:04.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.242][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:04.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:04.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:04.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.289][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:04.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:04.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.297][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:04.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.309][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:04.312][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:04.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:04.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:04.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:04.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:04.586][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-07 00:34:04.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:04.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:04.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:04.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:04.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:04.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:04.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:04.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:04.693][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-07 00:34:04.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:04.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-07 00:34:04.702][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:04.704][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:04.718][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:04.720][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:04.722][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:04.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:04.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:04.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:04.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:04.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:04.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:04.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:04.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:04.824][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-07 00:34:04.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:04.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:04.850][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-07 00:34:05.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-07 00:34:05.982][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:05.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-07 00:34:05.995][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-07 00:34:06.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-07 00:34:06.005][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:06.008][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:06.010][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:06.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:06.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:06.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:06.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:06.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:06.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:06.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:06.042][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.045][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.061][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:06.064][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:06.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:06.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.081][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:06.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:06.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:06.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:06.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:06.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:06.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.112][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:06.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:06.129][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:06.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:06.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:06.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.150][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:06.152][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:06.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.170][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:06.183][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.202][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:06.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.223][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:06.226][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:06.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:06.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:06.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.280][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:06.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:06.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:06.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.336][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:06.339][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:06.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:06.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:06.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:06.389][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:06.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:06.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:06.671][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-07 00:34:06.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:06.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:06.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:06.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:06.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:06.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:06.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:06.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:06.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:06.835][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-07 00:34:06.838][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:06.854][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-07 00:34:06.857][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:06.860][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:06.862][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:06.875][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:06.878][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:06.880][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:06.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:06.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:06.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:06.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:06.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:06.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:06.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:06.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-07 00:34:06.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:06.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:06.979][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-07 00:34:07.441][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-07 00:34:07.846][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:07.851][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-07 00:34:07.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-07 00:34:07.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-07 00:34:07.869][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:07.871][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:07.874][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:07.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:07.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:07.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:07.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:07.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:07.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:07.898][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.TRACE[2025-03-07 00:34:07.903][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:07.905][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:07.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:07.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:07.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.921][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:07.923][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:07.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:07.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:07.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.938][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:07.941][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:07.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:07.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:07.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.957][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:07.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:07.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:07.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:07.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:07.978][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:07.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:07.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:07.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:07.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:07.995][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:08.009][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:08.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.016][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:08.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.036][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:08.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:08.066][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:08.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:08.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:08.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.095][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:08.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:08.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:08.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:08.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.139][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:08.152][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:08.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.156][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:08.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:08.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.177][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:08.189][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:08.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.196][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:08.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:08.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:08.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:08.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:08.410][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-07 00:34:08.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:08.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:08.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:08.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:08.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:08.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:08.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:08.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:08.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:08.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:08.529][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-07 00:34:08.532][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:08.536][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-07 00:34:08.548][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:08.551][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:08.554][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:08.568][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:08.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:08.573][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:08.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:08.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:08.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:08.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:08.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:08.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:08.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:08.635][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-07 00:34:08.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:08.652][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:08.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-07 00:34:09.103][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-07 00:34:09.510][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:09.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-07 00:34:09.523][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-07 00:34:09.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-07 00:34:09.532][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:09.535][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:09.538][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:09.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:09.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:09.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:09.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:09.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:09.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:09.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:09.569][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:09.571][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:09.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:09.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.588][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:09.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:09.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.598][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:09.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.608][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:09.610][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:09.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:09.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:09.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.627][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:09.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:09.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:09.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:09.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:09.649][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:09.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:09.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.675][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:09.686][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:09.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.693][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:09.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:09.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.713][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:09.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:09.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.731][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:09.734][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:09.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.754][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:09.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.781][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:09.784][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:09.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:09.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:09.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.822][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:09.832][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:09.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.841][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:09.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.859][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:09.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:09.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:09.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:09.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:09.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:09.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:09.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:09.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:09.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:10.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:10.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:10.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:10.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:10.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:10.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:10.186][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-07 00:34:10.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:10.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:10.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:10.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:10.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:10.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:10.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:10.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:10.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:10.293][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-07 00:34:10.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:10.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-07 00:34:10.313][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:10.315][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:10.329][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:10.332][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:10.334][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:10.336][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:10.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:10.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:10.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:10.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:10.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:10.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:10.421][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-07 00:34:10.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:10.438][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:10.441][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-07 00:34:10.876][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-07 00:34:11.281][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:11.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-07 00:34:11.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-07 00:34:11.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-07 00:34:11.304][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:11.307][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:11.310][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:11.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:11.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:11.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:11.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:11.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:11.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:11.334][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.TRACE[2025-03-07 00:34:11.339][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.358][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:11.360][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:11.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:11.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.377][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:11.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:11.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.384][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:11.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:11.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:11.399][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:11.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:11.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:11.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:11.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.443][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:11.445][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:11.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.463][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:11.465][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.484][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:11.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:11.520][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:11.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:11.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.547][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:11.550][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:11.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:11.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:11.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.592][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:11.595][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:11.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.611][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:11.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:11.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.637][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:11.640][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:11.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.656][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:11.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:11.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:11.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:11.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:11.901][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-07 00:34:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:11.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:11.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:11.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:11.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:12.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:12.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:12.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:12.029][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-07 00:34:12.039][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:12.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-07 00:34:12.046][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:12.058][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:12.060][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:12.062][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:12.065][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:12.077][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:12.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:12.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:12.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:12.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:12.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:12.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:12.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:12.135][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-07 00:34:12.160][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:12.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:12.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-07 00:34:12.656][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-07 00:34:13.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:13.075][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-07 00:34:13.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-07 00:34:13.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-07 00:34:13.093][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:13.096][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:13.099][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:13.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:13.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:13.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:13.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:13.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:13.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:13.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:13.130][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.133][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.150][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:13.153][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:13.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.160][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:13.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.170][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:13.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:13.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:13.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:13.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.190][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:13.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:13.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:13.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:13.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:13.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:13.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:13.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:13.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.238][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:13.240][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:13.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.255][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:13.258][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.273][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:13.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.293][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:13.295][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:13.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:13.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.334][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:13.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:13.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.410][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:13.413][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:13.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:13.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:13.454][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:13.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.468][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:13.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:13.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:13.689][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-07 00:34:13.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:13.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:13.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:13.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:13.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:13.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:13.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:13.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:13.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:13.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:13.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:13.809][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-07 00:34:13.811][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:13.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-07 00:34:13.828][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:13.830][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:13.833][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:13.845][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:13.848][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:13.850][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:13.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:13.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:13.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:13.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:13.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:13.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:13.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:13.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-07 00:34:13.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:13.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:13.941][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-07 00:34:14.405][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-07 00:34:14.812][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:14.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-07 00:34:14.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-07 00:34:14.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-07 00:34:14.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:14.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:14.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:14.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:14.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:14.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:14.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:14.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:14.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:14.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:14.871][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:14.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:14.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.891][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:14.893][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:14.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.910][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:14.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:14.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:14.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:14.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.929][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:14.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:14.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.936][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:14.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:14.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.958][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:14.960][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:14.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:14.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:14.998][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:15.001][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:15.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.019][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:15.022][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.038][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:15.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.060][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:15.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:15.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:15.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:15.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.101][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:15.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:15.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:15.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:15.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.151][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:15.154][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:15.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.169][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.172][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:15.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:15.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.194][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:15.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:15.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:15.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:15.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:15.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:15.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:15.486][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-07 00:34:15.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:15.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:15.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:15.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:15.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:15.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:15.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:15.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:15.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:15.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:15.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:15.599][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-07 00:34:15.616][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:15.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-07 00:34:15.623][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:15.640][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:15.644][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:15.648][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:15.663][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:15.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:15.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:15.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:15.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:15.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:15.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:15.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:15.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:15.726][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-07 00:34:15.743][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:15.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:15.749][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-07 00:34:16.205][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-07 00:34:16.607][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:16.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-07 00:34:16.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-07 00:34:16.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-07 00:34:16.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:16.633][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:16.636][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:16.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:16.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:16.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:16.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:16.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:16.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:16.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:16.665][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:16.667][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:16.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:16.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.683][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:16.685][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:16.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.692][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:16.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.720][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:16.722][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:16.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:16.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.738][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:16.740][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:16.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:16.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:16.772][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:16.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.785][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.808][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:16.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:16.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.816][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.819][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:16.821][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:16.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.838][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:16.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.860][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:16.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:16.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:16.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:16.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.901][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:16.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:16.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:16.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.939][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:16.942][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:16.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.957][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:16.979][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:16.982][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:16.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:16.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:17.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:17.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:17.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:17.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:17.228][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-07 00:34:17.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:17.393][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:17.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:17.431][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:34:17.434][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:17.437][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 00:34:17.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:17.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:17.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:17.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:17.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:17.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:17.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:17.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:17.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:17.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:17.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:17.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:17.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:17.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:17.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:17.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:17.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:17.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:17.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:17.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:17.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:17.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:17.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:17.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:17.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:17.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:17.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:17.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:17.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:17.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:17.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:17.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:18.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:18.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:18.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:18.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:18.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:18.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:18.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:18.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:18.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:19.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:19.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:19.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:19.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:19.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:19.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:19.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:19.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:19.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:20.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:20.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:20.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:20.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:20.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:20.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:20.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:20.252][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:20.279][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:20.282][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:20.286][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:34:20.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:34:21.098][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:21.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-07 00:34:21.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-07 00:34:21.119][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[2025-03-07 00:34:21.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:21.143][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:21.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:34:21.553][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:34:21.975][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:21.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-07 00:34:21.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-07 00:34:21.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:21.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:21.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:22.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:22.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:22.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:22.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:22.018][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-07 00:34:22.020][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:22.024][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-07 00:34:22.027][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:22.029][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:22.031][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:22.034][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:22.036][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:22.038][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:22.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:22.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:22.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:22.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:22.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:22.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:22.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:22.068][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-07 00:34:22.074][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:22.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:22.080][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-07 00:34:22.513][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-07 00:34:23.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:23.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-07 00:34:23.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-07 00:34:23.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-07 00:34:23.030][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:23.032][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:23.035][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:23.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:23.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:23.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:23.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:23.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:23.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:23.059][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.TRACE[2025-03-07 00:34:23.064][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.082][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:23.085][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:23.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.091][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:23.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:23.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.100][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:23.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:23.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:23.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.159][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:23.161][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:23.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:23.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:23.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.177][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:23.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:23.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:23.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:23.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:23.199][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:23.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.214][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:23.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:23.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.223][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:23.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:23.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.258][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:23.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:23.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.281][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.284][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.288][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.310][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:23.325][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:23.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:23.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:23.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.365][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:23.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:23.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.372][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.385][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:23.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:23.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.407][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:23.413][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:23.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:23.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:23.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:23.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:23.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:23.655][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-07 00:34:23.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:23.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:23.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:23.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:23.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:23.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:23.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:23.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:23.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:23.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:23.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:23.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:23.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:23.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:23.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:23.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:23.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:23.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:23.869][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-07 00:34:23.895][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:23.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-07 00:34:23.906][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:23.919][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:23.922][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:23.925][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:23.928][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:23.936][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:23.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:23.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:23.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:23.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:23.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:23.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:23.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:24.000][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-07 00:34:24.020][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:24.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:24.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-07 00:34:24.456][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-07 00:34:24.874][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:24.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-07 00:34:24.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-07 00:34:24.893][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-07 00:34:24.896][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:24.899][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:24.902][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:24.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:24.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:24.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:24.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:24.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:24.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:24.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:24.931][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:24.933][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:24.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:24.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:24.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.949][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:24.951][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:24.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.959][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:24.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:24.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.967][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:24.970][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:24.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:24.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:24.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.987][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:24.989][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:24.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:24.993][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:24.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:24.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:25.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.005][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:25.007][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:25.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.046][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:25.049][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:25.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.132][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:25.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:25.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:25.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:25.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.165][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.168][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.207][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:25.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:25.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.224][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:25.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:25.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.247][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:25.258][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:25.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.266][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:25.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.289][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:25.302][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:25.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:25.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:25.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:25.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:25.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:25.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:25.579][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-07 00:34:25.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:25.766][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:25.787][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:25.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:34:25.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:25.813][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 00:34:25.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:25.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:25.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:25.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:25.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:25.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:25.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:25.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:25.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:25.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:25.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:25.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:25.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:26.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:26.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:26.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:26.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:26.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:26.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:26.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:26.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:26.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:26.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:27.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:27.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:27.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:27.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:27.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:27.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:27.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:27.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:27.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:27.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:27.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.609][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:28.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:28.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 00:34:28.624][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:28.630][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 00:34:28.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:28.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:28.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:28.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:28.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:28.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:28.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:28.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:28.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:28.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:29.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:29.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:29.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:29.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:29.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:29.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:29.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:29.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:29.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:29.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:30.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:30.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:30.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:30.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:30.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:30.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:30.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:30.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:31.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:31.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:31.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:31.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:31.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:31.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:31.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:31.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.362][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:31.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:34:31.439][biodb::testThat]
biodb.INFO [2025-03-07 00:34:31.442][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-07 00:34:31.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:31.458][biodb::testThat]
biodb.TRACE[2025-03-07 00:34:31.474][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 00:34:31.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 00:34:31.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:31.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:31.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:31.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:31.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:31.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:31.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:31.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:31.667][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:31.685][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:31.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 00:34:31.703][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:31.707][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 00:34:31.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:31.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:31.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:31.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:31.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:31.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:31.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:31.845][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:31.853][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:31.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 00:34:31.869][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:31.872][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 00:34:31.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:31.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:31.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:31.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:31.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:31.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:31.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:31.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:31.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:31.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:31.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:31.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:32.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:32.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:32.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:32.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:32.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:32.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:32.118][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:32.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:32.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:32.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:32.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:32.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:32.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:32.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.230][private$selectFields]
biodb.TRACE[2025-03-07 00:34:32.232][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:32.235][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:32.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.249][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.278][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.291][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.293][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.296][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.316][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.445][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 00:34:32.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:32.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:32.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:32.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:32.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:32.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:32.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.540][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.554][private$selectFields]
biodb.TRACE[2025-03-07 00:34:32.556][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:32.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:32.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.599][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.620][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.622][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.625][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.644][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:32.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.705][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:32.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:32.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:32.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:32.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:32.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:32.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:32.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:32.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.802][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.804][private$selectFields]
biodb.TRACE[2025-03-07 00:34:32.807][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:32.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:32.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.830][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.834][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.859][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:32.875][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.878][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.897][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:32.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:32.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:32.960][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 00:34:32.963][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:32.965][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:33.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:33.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:33.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:33.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:33.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:33.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:33.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:33.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:33.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:33.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:33.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:33.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:33.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:33.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:33.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:33.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:33.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:33.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:33.488][private$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[2025-03-07 00:34:33.927][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[2025-03-07 00:34:34.336][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:34.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-07 00:34:34.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-07 00:34:34.379][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[2025-03-07 00:34:34.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:34.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:34.394][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:34:34.811][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:34:35.209][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:35.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-07 00:34:35.223][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-07 00:34:35.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:35.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:35.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:35.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:35.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:35.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:35.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:35.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:35.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:35.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:35.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:35.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:35.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:35.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:35.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:35.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:35.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:35.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:35.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:35.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:35.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:35.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:35.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:35.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:35.567][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:35.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:35.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:35.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:35.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:35.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:35.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:35.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:35.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:35.808][private$selectFields]
biodb.TRACE[2025-03-07 00:34:35.811][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:35.813][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:35.815][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:35.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.835][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.858][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:35.869][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:35.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.874][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.892][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:35.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:35.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:35.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:35.963][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 00:34:35.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:35.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:35.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:36.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:36.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:36.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:36.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:36.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.337][private$selectFields]
biodb.TRACE[2025-03-07 00:34:36.339][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:36.352][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:36.354][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.391][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.498][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.526][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:36.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.576][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:36.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:36.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:36.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:36.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:36.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:36.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:36.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:36.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.674][private$selectFields]
biodb.TRACE[2025-03-07 00:34:36.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:36.679][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:36.681][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.705][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.725][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.728][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:36.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.733][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.753][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:36.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:36.848][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 00:34:36.850][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:36.853][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:36.901][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:36.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:36.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:34:36.957][biodb::testThat]
biodb.INFO [2025-03-07 00:34:36.959][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-07 00:34:36.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:36.974][biodb::testThat]
biodb.TRACE[2025-03-07 00:34:36.980][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 00:34:36.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 00:34:36.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:36.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:37.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:37.157][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:37.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:37.180][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 00:34:37.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:37.186][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 00:34:37.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:37.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:37.306][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:37.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 00:34:37.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:37.317][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 00:34:37.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:37.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:37.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:37.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:37.500][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:37.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:37.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.545][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.547][private$selectFields]
biodb.TRACE[2025-03-07 00:34:37.549][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:37.551][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:37.555][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.557][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.581][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.588][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.595][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:37.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.639][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 00:34:37.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:37.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:37.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:37.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:37.671][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[2025-03-07 00:34:37.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.824][private$selectFields]
biodb.TRACE[2025-03-07 00:34:37.826][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:37.828][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:37.839][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.844][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.896][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.899][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:37.901][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.917][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:37.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:37.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:37.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:37.978][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:37.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:37.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:37.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.084][private$selectFields]
biodb.TRACE[2025-03-07 00:34:38.087][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:38.090][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:38.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.112][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.131][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.182][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.204][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:38.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.278][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 00:34:38.281][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:38.292][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:38.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:38.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:38.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:38.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:38.471][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:38.494][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:38.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 00:34:38.500][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:38.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 00:34:38.511][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:38.519][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:38.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 00:34:38.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:38.528][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 00:34:38.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:38.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:38.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:38.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:38.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:38.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:38.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:38.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:38.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:38.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:38.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:38.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:38.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:38.857][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:38.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:38.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:38.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:38.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:38.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:38.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:38.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:38.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.953][private$selectFields]
biodb.TRACE[2025-03-07 00:34:38.955][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:38.957][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:38.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:38.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.975][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:38.981][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:38.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:38.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.011][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.013][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.031][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.098][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 00:34:39.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:39.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:39.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:39.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:39.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:39.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:39.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:39.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.202][private$selectFields]
biodb.TRACE[2025-03-07 00:34:39.204][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:39.216][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:39.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.224][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.242][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.256][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.259][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.261][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.275][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.299][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:39.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:39.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:39.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:39.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:39.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:39.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:39.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:39.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:39.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.481][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.485][private$selectFields]
biodb.TRACE[2025-03-07 00:34:39.488][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:39.490][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:39.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.553][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.555][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:39.566][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.569][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:39.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:39.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.657][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 00:34:39.667][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:39.670][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:39.710][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:39.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:34:39.745][biodb::testThat]
biodb.INFO [2025-03-07 00:34:39.747][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-07 00:34:39.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:39.751][biodb::testThat]
biodb.TRACE[2025-03-07 00:34:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 00:34:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 00:34:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:39.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:39.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:39.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:39.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:39.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:39.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:39.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:39.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:39.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:39.930][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:39.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:39.951][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 00:34:39.954][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:39.967][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 00:34:39.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:39.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:39.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:40.095][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:40.102][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:40.115][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 00:34:40.118][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:40.121][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 00:34:40.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:40.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:40.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:40.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:40.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:40.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:40.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:40.381][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:40.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:40.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:40.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.491][private$selectFields]
biodb.TRACE[2025-03-07 00:34:40.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:40.507][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:40.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.543][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.566][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.592][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:40.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.668][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 00:34:40.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:40.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:40.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.769][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.783][private$selectFields]
biodb.TRACE[2025-03-07 00:34:40.786][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:40.788][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:40.791][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.793][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.812][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.832][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.834][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.846][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:40.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.850][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.871][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:40.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.930][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:40.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:40.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:40.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:40.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:40.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:40.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:40.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:40.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:40.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.015][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:41.017][private$selectFields]
biodb.TRACE[2025-03-07 00:34:41.030][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:41.033][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:41.035][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:41.038][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.080][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:41.082][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:41.095][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.112][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:41.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.173][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 00:34:41.175][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:41.183][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:41.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:41.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:41.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:41.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:41.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:41.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:41.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:41.440][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:41.457][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:41.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 00:34:41.470][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:41.473][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 00:34:41.489][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:41.496][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:41.516][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 00:34:41.519][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:41.522][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 00:34:41.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:41.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:41.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:41.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:41.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:41.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:41.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:41.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:41.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:41.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:41.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:41.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:41.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:41.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:41.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:41.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:41.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:41.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:41.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:41.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:41.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:41.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:41.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:41.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:41.879][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 00:34:41.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:41.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:41.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:41.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:41.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:41.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:41.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:41.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:41.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:41.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:41.983][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:41.995][private$selectFields]
biodb.TRACE[2025-03-07 00:34:41.997][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:41.999][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:42.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.003][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.020][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.024][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.057][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.060][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.101][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:42.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.174][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 00:34:42.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:42.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:42.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:42.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:42.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:42.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:42.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:42.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.322][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.325][private$selectFields]
biodb.TRACE[2025-03-07 00:34:42.355][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:42.358][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:42.360][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.362][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.383][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.404][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.406][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.436][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.498][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 00:34:42.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:42.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:42.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:42.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:42.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:42.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:42.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:42.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.584][private$selectFields]
biodb.TRACE[2025-03-07 00:34:42.596][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 00:34:42.598][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 00:34:42.600][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.602][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.622][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.624][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.639][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.641][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.643][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 00:34:42.655][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.658][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.663][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 00:34:42.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:42.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:42.726][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 00:34:42.736][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 00:34:42.739][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 00:34:42.849][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:42.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 00:34:42.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:42.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 00:34:42.874][biodb::testThat]
biodb.INFO [2025-03-07 00:34:42.892][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-07 00:34:42.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:42.898][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:42.921][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-07 00:34:42.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:34:42.927][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-07 00:34:42.930][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:34:42.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:34:42.952][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:42.955][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:42.957][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:42.976][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:42.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:43.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:43.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:43.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:43.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:43.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:43.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:43.058][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-07 00:34:43.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:43.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:43.077][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-07 00:34:43.736][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-07 00:34:44.185][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:44.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-07 00:34:44.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-07 00:34:44.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-07 00:34:44.208][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:44.210][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:34:44.213][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:44.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:44.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:44.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:44.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:44.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:44.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:44.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:44.243][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.245][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.261][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:44.264][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:44.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.270][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:44.273][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:44.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:44.282][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:44.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:44.305][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:44.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:44.314][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:44.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.321][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:44.335][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:44.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.342][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:44.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:44.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.363][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:44.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:44.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.385][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:44.392][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:44.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.400][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:44.412][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:44.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:44.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:44.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:44.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:44.641][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-07 00:34:44.655][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-07 00:34:44.712][biodb::testThat]
biodb.INFO [2025-03-07 00:34:44.716][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-07 00:34:44.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:44.726][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:44.760][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-07 00:34:44.776][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-07 00:34:44.779][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-07 00:34:44.796][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-07 00:34:44.800][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-03-07 00:34:44.804][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-03-07 00:34:44.822][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:34:44.824][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:44.827][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:34:44.840][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:34:44.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:44.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:44.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:44.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:44.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:44.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:44.903][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[2025-03-07 00:34:44.907][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-07 00:34:44.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:44.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:44.957][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-07 00:34:45.389][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-07 00:34:45.825][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:45.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-07 00:34:45.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-07 00:34:45.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:45.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:45.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:45.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:45.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:45.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:45.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:45.865][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-07 00:34:45.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:45.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:45.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-07 00:34:46.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-07 00:34:46.758][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:46.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-07 00:34:46.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-07 00:34:46.776][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-07 00:34:46.780][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:34:46.782][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-07 00:34:46.785][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-07 00:34:46.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:46.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:46.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:46.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:46.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:46.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:46.808][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[2025-03-07 00:34:46.813][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:46.815][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:46.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:46.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:46.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.830][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:46.833][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:46.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.839][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:46.842][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:46.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:46.851][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:46.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.857][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:46.860][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:46.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:46.869][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:46.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.875][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:46.878][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:46.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:46.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:46.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.891][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.893][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:46.896][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:46.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.903][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:46.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:46.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.912][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:46.915][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:46.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:46.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:46.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:46.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:46.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:46.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:46.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:47.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:47.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:47.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:47.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:47.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:47.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:47.083][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[2025-03-07 00:34:47.098][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.101][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.133][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:47.136][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:47.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.153][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:47.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:47.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:47.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:47.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.203][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:47.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:47.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:47.226][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:47.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.239][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:47.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:47.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.258][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.260][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.300][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.306][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.344][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:47.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:47.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.362][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:47.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:47.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.381][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:47.383][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:47.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:47.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.425][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:47.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:47.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.432][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:47.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:47.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.464][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:47.466][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:47.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:47.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.494][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:47.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:47.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:47.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:47.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:47.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:47.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:47.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:47.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:47.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:47.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:47.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:47.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:34:47.768][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.772][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:47.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:47.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.812][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:47.816][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:47.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:34:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:34:47.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.847][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:47.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:47.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:34:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:34:47.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:47.890][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:47.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:34:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:34:47.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.939][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.941][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:34:47.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.980][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.982][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:47.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:47.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:47.989][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:48.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:34:48.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.016][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:48.026][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:48.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.034][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:34:48.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:34:48.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.068][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:48.072][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:48.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:48.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:48.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.098][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:48.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:48.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:48.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:48.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.150][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:48.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:48.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.170][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:34:48.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:34:48.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.191][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:48.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:48.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.216][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:34:48.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:34:48.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:34:48.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:34:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:34:48.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:48.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:34:48.533][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-07 00:34:48.536][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-07 00:34:48.538][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-07 00:34:48.594][biodb::testThat]
biodb.INFO [2025-03-07 00:34:48.608][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-07 00:34:48.611][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:48.613][biodb::testThat]
biodb.INFO [2025-03-07 00:34:48.758][biodb::testThat]
biodb.INFO [2025-03-07 00:34:48.772][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-07 00:34:48.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:48.777][biodb::testThat]
biodb.INFO [2025-03-07 00:34:48.818][biodb::testThat]
biodb.INFO [2025-03-07 00:34:48.821][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-07 00:34:48.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:48.837][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:48.842][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[2025-03-07 00:34:48.863][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:48.865][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:48.879][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:34:49.445][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:34:50.022][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:50.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-07 00:34:50.038][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-07 00:34:50.070][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:34:50.074][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:34:50.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:50.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:34:50.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:50.086][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:34:50.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:34:50.092][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 00:34:50.095][biodb::testThat]
biodb.INFO [2025-03-07 00:34:50.098][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-07 00:34:50.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:50.103][biodb::testThat]
biodb.ERROR[2025-03-07 00:34:50.138][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-07 00:34:50.181][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-07 00:34:50.248][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 00:34:50.253][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 00:34:50.265][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 00:34:50.268][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 00:34:50.271][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:50.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:50.287][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:50.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:50.324][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 00:34:50.384][biodb::testContext]
biodb.INFO [2025-03-07 00:34:50.386][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:34:50.388][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-07 00:34:50.402][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:34:50.404][biodb::testContext]
biodb.INFO [2025-03-07 00:34:50.409][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:34:50.423][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 00:34:50.444][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:50.446][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 00:34:50.448][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.466][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 00:34:50.469][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.487][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 00:34:50.489][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.507][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 00:34:50.509][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 00:34:50.523][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 00:34:50.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.556][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 00:34:50.560][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 00:34:50.562][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.579][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 00:34:50.581][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 00:34:50.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.599][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 00:34:50.601][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 00:34:50.604][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 00:34:50.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.620][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[2025-03-07 00:34:50.622][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 00:34:50.632][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.640][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 00:34:50.654][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 00:34:50.657][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 00:34:50.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.679][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:34:50.681][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 00:34:50.684][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 00:34:50.686][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 00:34:50.698][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 00:34:50.701][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 00:34:50.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.719][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 00:34:50.721][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 00:34:50.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.737][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 00:34:50.739][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 00:34:50.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.756][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 00:34:50.758][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 00:34:50.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.774][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 00:34:50.776][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 00:34:50.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.795][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 00:34:50.797][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 00:34:50.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.817][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:34:50.819][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 00:34:50.861][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 00:34:50.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.868][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 00:34:50.871][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 00:34:50.873][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 00:34:50.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:50.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:50.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:50.881][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 00:34:50.885][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:50.887][self$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[2025-03-07 00:34:50.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:50.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:50.897][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:50.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:50.902][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:50.914][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:50.917][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:34:50.921][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:50.924][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:50.936][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 00:34:50.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:50.941][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:50.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:50.954][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:50.954][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:50.954][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:50.954][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:34:50.954][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:34:50.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:50.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:50.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:50.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:50.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:50.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:50.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:50.981][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:50.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:50.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:50.998][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.001][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.012][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 00:34:51.016][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.018][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:34:51.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:51.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.036][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.055][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:34:51.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:51.060][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.072][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 00:34:51.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:51.077][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.079][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.089][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:51.089][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:51.089][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:51.089][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:34:51.089][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:34:51.091][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:51.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:51.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.115][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:51.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:51.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.136][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.147][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 00:34:51.151][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.153][self$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[2025-03-07 00:34:51.155][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:51.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.172][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.175][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.187][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.189][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:34:51.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:51.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.195][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 00:34:51.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:51.207][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.210][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.213][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:51.225][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:51.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.244][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.246][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:51.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:51.264][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.266][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.270][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 00:34:51.284][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.286][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:34:51.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:51.302][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.304][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.309][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.320][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:34:51.323][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:51.325][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.327][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 00:34:51.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:51.342][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:51.346][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.356][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:51.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.363][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:51.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:51.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:51.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:51.382][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:51.395][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:51.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:51.400][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:51.403][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:51.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.417][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[2025-03-07 00:34:51.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.536][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.DEBUG[2025-03-07 00:34:51.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.631][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[2025-03-07 00:34:51.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.652][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[2025-03-07 00:34:51.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:51.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:51.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:51.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:51.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:51.759][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 00:34:51.767][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 00:34:51.770][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 00:34:51.773][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 00:34:51.802][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:34:51.806][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 00:34:51.809][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 00:34:51.819][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 00:34:51.822][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 00:34:51.825][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 00:34:51.836][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:34:51.840][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 00:34:51.843][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 00:34:51.856][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 00:34:51.859][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 00:34:51.862][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 00:34:51.874][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 00:34:51.878][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 00:34:51.881][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:34:51.909][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 00:34:51.913][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 00:34:51.916][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 00:34:51.938][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 00:34:51.941][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 00:34:51.945][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 00:34:51.958][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 00:34:51.962][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 00:34:51.967][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 00:34:51.980][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 00:34:51.984][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 00:34:51.987][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 00:34:52.001][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 00:34:52.004][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 00:34:52.007][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 00:34:52.019][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 00:34:52.023][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 00:34:52.026][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 00:34:52.051][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 00:34:52.055][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 00:34:52.067][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 00:34:52.070][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 00:34:52.074][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 00:34:52.087][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 00:34:52.091][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 00:34:52.094][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 00:34:52.107][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 00:34:52.111][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 00:34:52.114][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 00:34:52.126][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 00:34:52.129][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 00:34:52.132][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 00:34:52.144][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 00:34:52.147][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 00:34:52.150][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 00:34:52.153][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 00:34:52.157][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 00:34:52.160][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 00:34:52.186][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 00:34:52.190][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 00:34:52.193][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 00:34:52.205][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 00:34:52.208][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 00:34:52.212][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 00:34:52.224][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 00:34:52.227][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 00:34:52.230][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 00:34:52.242][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:34:52.245][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:34:52.249][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 00:34:52.262][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 00:34:52.266][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 00:34:52.269][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 00:34:52.295][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 00:34:52.298][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 00:34:52.302][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 00:34:52.314][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 00:34:52.317][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 00:34:52.321][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 00:34:52.335][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 00:34:52.346][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 00:34:52.349][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 00:34:52.361][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 00:34:52.365][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 00:34:52.368][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 00:34:52.374][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:34:52.376][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:52.378][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.382][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.417][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[2025-03-07 00:34:52.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.847][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[2025-03-07 00:34:52.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:52.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:52.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:52.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:52.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:52.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:52.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:52.949][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 00:34:52.953][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 00:34:52.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:52.971][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 00:34:52.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:52.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:52.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:52.989][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:52.992][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:52.994][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 00:34:53.007][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 00:34:53.009][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:53.012][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:53.014][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 00:34:53.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 00:34:53.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 00:34:53.030][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:53.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:53.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:53.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:53.034][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 00:34:53.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:53.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:53.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:53.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:53.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:53.071][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:53.073][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:53.073][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 00:34:53.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:53.077][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:53.090][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:53.093][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 00:34:53.093][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 00:34:53.096][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:34:53.107][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:34:53.111][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 00:34:53.114][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:34:53.127][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:34:53.131][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:34:53.146][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 00:34:53.149][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 00:34:53.152][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 00:34:53.173][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 00:34:53.176][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:34:53.179][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:34:53.192][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 00:34:53.195][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 00:34:53.197][biodb::testThat]
biodb.INFO [2025-03-07 00:34:53.200][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-07 00:34:53.213][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:53.217][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:53.230][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 00:34:53.247][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 00:34:53.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.264][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 00:34:53.284][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:53.311][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 00:34:53.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.322][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 00:34:53.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:53.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:53.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 00:34:53.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.407][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 00:34:53.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.459][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[2025-03-07 00:34:53.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:53.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:53.676][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.679][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 00:34:53.688][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.691][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 00:34:53.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:53.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:53.776][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.779][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 00:34:53.782][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.785][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 00:34:53.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.838][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[2025-03-07 00:34:53.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:53.896][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:53.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:53.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 00:34:53.939][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:53.942][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 00:34:53.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:53.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:53.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:53.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:53.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:53.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:53.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:54.006][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:54.014][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:54.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 00:34:54.031][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:54.035][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 00:34:54.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:54.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:54.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:54.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:54.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:54.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:54.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:54.114][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:54.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:34:54.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-03-07 00:34:54.137][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:34:54.141][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-03-07 00:34:54.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:54.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:54.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:54.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:54.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:54.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:54.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 00:34:54.239][biodb::testThat]
biodb.INFO [2025-03-07 00:34:54.241][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-07 00:34:54.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:54.246][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:54.263][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:34:54.277][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:54.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:54.300][private$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[2025-03-07 00:34:54.798][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[2025-03-07 00:34:55.204][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:55.208][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-07 00:34:55.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-07 00:34:55.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:55.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:55.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:55.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:55.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:55.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:55.243][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[2025-03-07 00:34:55.251][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[2025-03-07 00:34:55.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:55.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:55.265][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-07 00:34:55.663][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-07 00:34:56.073][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:34:56.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-07 00:34:56.087][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-07 00:34:56.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:34:56.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:56.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:56.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:56.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:56.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 00:34:56.127][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 00:34:56.130][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 00:34:56.132][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 00:34:56.134][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 00:34:56.137][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:56.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:56.141][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:56.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:56.145][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 00:34:56.156][biodb::testContext]
biodb.INFO [2025-03-07 00:34:56.159][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:34:56.161][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-07 00:34:56.164][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:34:56.167][biodb::testContext]
biodb.INFO [2025-03-07 00:34:56.172][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:34:56.176][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 00:34:56.184][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:56.187][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 00:34:56.189][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.209][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 00:34:56.212][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.231][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 00:34:56.233][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.250][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 00:34:56.252][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 00:34:56.255][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 00:34:56.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.272][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 00:34:56.275][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 00:34:56.286][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.312][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 00:34:56.315][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 00:34:56.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.332][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 00:34:56.335][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 00:34:56.337][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 00:34:56.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.355][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 00:34:56.357][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.377][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 00:34:56.379][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 00:34:56.381][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 00:34:56.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.400][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:34:56.410][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 00:34:56.413][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 00:34:56.415][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 00:34:56.418][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 00:34:56.435][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 00:34:56.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.452][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 00:34:56.454][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 00:34:56.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.475][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 00:34:56.478][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 00:34:56.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.496][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 00:34:56.498][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 00:34:56.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.517][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 00:34:56.530][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 00:34:56.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.539][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 00:34:56.555][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 00:34:56.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.575][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:34:56.578][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 00:34:56.601][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 00:34:56.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:56.610][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 00:34:56.612][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 00:34:56.615][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 00:34:56.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:56.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:56.632][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[2025-03-07 00:34:56.635][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 00:34:56.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.652][self$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[2025-03-07 00:34:56.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:56.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.672][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:34:56.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:56.700][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.702][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 00:34:56.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:56.714][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.716][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.718][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:56.718][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:56.718][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:56.718][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:34:56.718][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:34:56.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:56.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:56.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:56.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:56.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:56.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:56.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.755][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:56.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:56.762][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.783][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.786][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 00:34:56.790][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:34:56.805][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.808][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:56.811][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.826][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.831][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:34:56.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:56.846][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.849][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 00:34:56.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:56.918][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:56.923][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:56.923][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:56.923][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:56.923][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:34:56.923][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:34:56.948][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:56.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:56.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:56.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:56.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:56.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:56.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:56.975][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:56.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:56.988][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:56.991][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:56.993][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 00:34:57.008][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.010][self$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[2025-03-07 00:34:57.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:57.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.045][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:34:57.068][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:57.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.072][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 00:34:57.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:57.082][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.084][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.086][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:57.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:57.101][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:57.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:57.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:57.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:57.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.119][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:57.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:57.136][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.139][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.141][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 00:34:57.157][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.160][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:34:57.164][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.166][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:57.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:34:57.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:57.207][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.210][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 00:34:57.221][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:57.223][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.225][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:57.227][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:34:57.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:57.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:57.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:57.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:57.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:57.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:57.266][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:57.295][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:57.300][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:57.303][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:34:57.319][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:57.321][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.323][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.DEBUG[2025-03-07 00:34:57.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.343][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[2025-03-07 00:34:57.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.362][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.DEBUG[2025-03-07 00:34:57.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.381][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[2025-03-07 00:34:57.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.485][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.DEBUG[2025-03-07 00:34:57.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.627][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[2025-03-07 00:34:57.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.671][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[2025-03-07 00:34:57.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:57.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:57.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:57.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:57.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:57.709][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 00:34:57.722][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 00:34:57.726][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 00:34:57.738][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 00:34:57.741][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:34:57.745][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 00:34:57.761][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 00:34:57.765][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 00:34:57.781][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 00:34:57.786][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 00:34:57.790][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:34:57.820][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 00:34:57.824][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 00:34:57.842][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 00:34:57.846][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 00:34:57.859][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 00:34:57.862][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 00:34:57.866][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 00:34:57.880][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:34:57.884][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 00:34:57.899][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 00:34:57.903][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 00:34:57.906][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 00:34:57.939][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 00:34:57.942][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 00:34:57.946][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 00:34:57.971][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 00:34:57.975][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 00:34:57.993][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 00:34:57.998][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 00:34:58.002][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 00:34:58.016][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 00:34:58.019][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 00:34:58.033][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 00:34:58.037][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 00:34:58.041][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 00:34:58.045][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 00:34:58.048][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 00:34:58.052][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 00:34:58.077][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 00:34:58.080][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 00:34:58.090][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 00:34:58.094][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 00:34:58.097][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 00:34:58.107][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 00:34:58.111][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 00:34:58.115][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 00:34:58.127][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 00:34:58.131][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 00:34:58.134][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 00:34:58.148][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 00:34:58.152][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 00:34:58.177][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 00:34:58.185][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 00:34:58.192][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 00:34:58.196][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 00:34:58.199][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 00:34:58.213][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 00:34:58.217][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 00:34:58.231][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 00:34:58.234][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 00:34:58.237][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 00:34:58.241][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 00:34:58.244][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 00:34:58.247][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 00:34:58.260][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 00:34:58.264][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:34:58.267][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:34:58.298][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 00:34:58.304][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 00:34:58.308][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 00:34:58.315][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 00:34:58.319][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 00:34:58.323][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 00:34:58.338][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 00:34:58.341][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 00:34:58.355][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 00:34:58.359][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 00:34:58.362][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 00:34:58.375][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 00:34:58.378][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 00:34:58.390][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 00:34:58.393][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 00:34:58.396][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 00:34:58.412][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:34:58.416][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:34:58.418][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.439][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.441][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[2025-03-07 00:34:58.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.465][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[2025-03-07 00:34:58.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.825][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[2025-03-07 00:34:58.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.919][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[2025-03-07 00:34:58.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:58.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:58.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:58.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:58.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:58.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:58.990][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.DEBUG[2025-03-07 00:34:58.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:58.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:59.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:59.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:59.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:59.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:59.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:59.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:34:59.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:34:59.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:34:59.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:34:59.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:34:59.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:34:59.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:34:59.083][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 00:34:59.087][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 00:34:59.103][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:59.105][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 00:34:59.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:59.121][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:34:59.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:59.127][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:34:59.139][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:59.142][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 00:34:59.145][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 00:34:59.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:34:59.161][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:59.164][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 00:34:59.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 00:34:59.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 00:34:59.174][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 00:34:59.177][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:34:59.177][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:34:59.177][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:34:59.180][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 00:34:59.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:59.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:59.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:34:59.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:34:59.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:34:59.211][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:34:59.224][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:34:59.224][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 00:34:59.227][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:34:59.230][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:34:59.232][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 00:34:59.244][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 00:34:59.244][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 00:34:59.247][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:34:59.252][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:34:59.268][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 00:34:59.272][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:34:59.292][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:34:59.296][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:34:59.318][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 00:34:59.321][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 00:34:59.334][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 00:34:59.338][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 00:34:59.341][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:34:59.344][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:34:59.354][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 00:34:59.357][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 00:34:59.360][biodb::testThat]
biodb.INFO [2025-03-07 00:34:59.375][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-07 00:34:59.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:34:59.381][biodb::testThat]
biodb.DEBUG[2025-03-07 00:34:59.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.INFO [2025-03-07 00:34:59.414][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-07 00:34:59.418][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:34:59.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:34:59.452][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-07 00:34:59.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-07 00:35:00.412][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:35:00.417][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-07 00:35:00.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-07 00:35:00.433][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 00:35:00.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:35:00.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:35:00.447][private$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[2025-03-07 00:35:00.850][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[2025-03-07 00:35:01.248][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:35:01.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-07 00:35:01.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-07 00:35:01.281][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 00:35:01.283][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 00:35:01.286][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 00:35:01.288][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 00:35:01.290][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:01.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:01.294][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:01.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:01.298][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 00:35:01.307][biodb::testContext]
biodb.INFO [2025-03-07 00:35:01.310][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:35:01.312][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-07 00:35:01.314][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 00:35:01.316][biodb::testContext]
biodb.INFO [2025-03-07 00:35:01.320][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:35:01.324][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 00:35:01.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:35:01.334][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 00:35:01.336][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.344][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 00:35:01.347][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.355][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 00:35:01.357][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.365][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 00:35:01.367][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 00:35:01.369][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 00:35:01.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.375][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[2025-03-07 00:35:01.377][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 00:35:01.380][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 00:35:01.382][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.390][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 00:35:01.392][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 00:35:01.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.411][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 00:35:01.413][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 00:35:01.415][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 00:35:01.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.438][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 00:35:01.441][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.457][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 00:35:01.470][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 00:35:01.472][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 00:35:01.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.490][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:35:01.493][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 00:35:01.496][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 00:35:01.498][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 00:35:01.500][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 00:35:01.513][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 00:35:01.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.530][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 00:35:01.533][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 00:35:01.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.552][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 00:35:01.555][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 00:35:01.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.570][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 00:35:01.573][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 00:35:01.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.592][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 00:35:01.594][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 00:35:01.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.612][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 00:35:01.614][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 00:35:01.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.631][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 00:35:01.634][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 00:35:01.666][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 00:35:01.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 00:35:01.677][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 00:35:01.680][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 00:35:01.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:01.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:01.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:01.689][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 00:35:01.694][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.696][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 00:35:01.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.710][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:35:01.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.715][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.725][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.730][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:35:01.732][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:35:01.745][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.748][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 00:35:01.750][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:35:01.752][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.766][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:35:01.766][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:35:01.766][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:35:01.766][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:35:01.766][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:35:01.769][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:35:01.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:01.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:01.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:35:01.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:01.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:01.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.799][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.801][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:35:01.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:35:01.806][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.823][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.826][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 00:35:01.831][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.840][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:35:01.843][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:35:01.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.850][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.870][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:35:01.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:35:01.885][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.887][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 00:35:01.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:35:01.892][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.907][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:35:01.907][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:35:01.907][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:35:01.907][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 00:35:01.907][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 00:35:01.913][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:35:01.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:01.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:01.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:35:01.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:01.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:01.943][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:35:01.945][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:35:01.960][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:35:01.962][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:01.965][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:01.977][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 00:35:01.983][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:01.986][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 00:35:01.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:35:02.004][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.009][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.014][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 00:35:02.016][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:35:02.019][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.032][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 00:35:02.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:35:02.037][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.040][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.076][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.079][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:35:02.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:02.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:02.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:35:02.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:02.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:02.167][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.170][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:35:02.186][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:35:02.189][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.191][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.201][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 00:35:02.205][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.208][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 00:35:02.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:35:02.222][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.225][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.241][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.243][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 00:35:02.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:35:02.248][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.260][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 00:35:02.262][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:35:02.265][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.267][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:02.279][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.282][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 00:35:02.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:02.286][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:02.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:35:02.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:02.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:02.309][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:35:02.312][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:35:02.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:35:02.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:02.329][self$setPropertyValue]
biodb.DEBUG[2025-03-07 00:35:02.341][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:35:02.343][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.345][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[2025-03-07 00:35:02.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.671][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[2025-03-07 00:35:02.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:02.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:02.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:02.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:02.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:02.751][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 00:35:02.755][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 00:35:02.766][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 00:35:02.770][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 00:35:02.773][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:35:02.791][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 00:35:02.796][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 00:35:02.814][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 00:35:02.818][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 00:35:02.822][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 00:35:02.834][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:35:02.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 00:35:02.841][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 00:35:02.853][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 00:35:02.857][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 00:35:02.860][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 00:35:02.873][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 00:35:02.877][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 00:35:02.880][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:35:02.894][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 00:35:02.898][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 00:35:02.901][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 00:35:02.919][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 00:35:02.923][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 00:35:02.946][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 00:35:02.951][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 00:35:02.954][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 00:35:02.971][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 00:35:02.974][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 00:35:02.978][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 00:35:02.991][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 00:35:02.995][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 00:35:02.998][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 00:35:03.016][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 00:35:03.019][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 00:35:03.033][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 00:35:03.036][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 00:35:03.040][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 00:35:03.056][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 00:35:03.061][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 00:35:03.065][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 00:35:03.079][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 00:35:03.083][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 00:35:03.086][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 00:35:03.098][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 00:35:03.102][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 00:35:03.105][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 00:35:03.119][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 00:35:03.124][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 00:35:03.137][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 00:35:03.140][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 00:35:03.144][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 00:35:03.157][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 00:35:03.160][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 00:35:03.164][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 00:35:03.180][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 00:35:03.184][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 00:35:03.188][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 00:35:03.201][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 00:35:03.205][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 00:35:03.208][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 00:35:03.223][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 00:35:03.226][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 00:35:03.241][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 00:35:03.244][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 00:35:03.248][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 00:35:03.257][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:35:03.261][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:35:03.264][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 00:35:03.279][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 00:35:03.283][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 00:35:03.287][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 00:35:03.304][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 00:35:03.308][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 00:35:03.313][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 00:35:03.328][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 00:35:03.331][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 00:35:03.344][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 00:35:03.347][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 00:35:03.351][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 00:35:03.364][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 00:35:03.367][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 00:35:03.371][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 00:35:03.385][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 00:35:03.388][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 00:35:03.391][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 00:35:03.393][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.406][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.573][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[2025-03-07 00:35:03.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.847][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[2025-03-07 00:35:03.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.883][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[2025-03-07 00:35:03.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:03.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:03.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:03.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 00:35:03.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 00:35:03.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:03.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:03.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:04.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:04.015][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[2025-03-07 00:35:04.019][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 00:35:04.023][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 00:35:04.039][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:04.043][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 00:35:04.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:04.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 00:35:04.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:04.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 00:35:04.074][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:04.085][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 00:35:04.088][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 00:35:04.090][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 00:35:04.104][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:04.107][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 00:35:04.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 00:35:04.113][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 00:35:04.125][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 00:35:04.128][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 00:35:04.128][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 00:35:04.128][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 00:35:04.131][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 00:35:04.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:04.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:04.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 00:35:04.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 00:35:04.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 00:35:04.167][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 00:35:04.171][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:35:04.171][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 00:35:04.174][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 00:35:04.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 00:35:04.194][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 00:35:04.197][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 00:35:04.197][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 00:35:04.205][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 00:35:04.209][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 00:35:04.231][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 00:35:04.235][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 00:35:04.240][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 00:35:04.254][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 00:35:04.268][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 00:35:04.271][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 00:35:04.275][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 00:35:04.294][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 00:35:04.298][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:35:04.300][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 00:35:04.305][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 00:35:04.307][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 00:35:04.311][biodb::testThat]
biodb.INFO [2025-03-07 00:35:04.326][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-07 00:35:04.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 00:35:04.331][biodb::testThat]
biodb.DEBUG[2025-03-07 00:35:04.349][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 00:35:04.366][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:35:04.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 00:35:04.373][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:35:04.392][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 00:35:04.413][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[2025-03-07 00:35:04.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 00:35:04.443][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-07 00:35:04.446][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 00:35:04.450][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-07 00:35:04.463][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-07 00:35:04.476][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 00:35:04.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-07 00:35:04.483][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 00:35:04.497][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 00:35:04.500][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 00:35:04.503][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 00:35:04.516][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 00:35:04.519][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 00:35:04.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:35:04.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:04.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:04.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:04.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:04.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:04.585][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[2025-03-07 00:35:04.599][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-07 00:35:04.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 00:35:04.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 00:35:04.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-07 00:35:06.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-07 00:35:06.820][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 00:35:06.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-07 00:35:06.834][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-07 00:35:06.840][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-07 00:35:06.845][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 00:35:06.848][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 00:35:06.851][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 00:35:06.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 00:35:06.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:06.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:06.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:06.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:06.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:06.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 00:35:06.886][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:06.889][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:06.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:06.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:06.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.906][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:35:06.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:35:06.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.916][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 00:35:06.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 00:35:06.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.925][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:35:06.928][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:35:06.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 00:35:06.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 00:35:06.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.945][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 00:35:06.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 00:35:06.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.952][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.955][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 00:35:06.957][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 00:35:06.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.965][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:35:06.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:35:06.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.980][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:35:06.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 00:35:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:06.996][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:35:06.999][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:35:07.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.017][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 00:35:07.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 00:35:07.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.036][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:35:07.039][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:35:07.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:35:07.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 00:35:07.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.073][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:35:07.075][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:35:07.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.091][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 00:35:07.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 00:35:07.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.109][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:35:07.112][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:35:07.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.129][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 00:35:07.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 00:35:07.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.158][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:35:07.161][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:35:07.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 00:35:07.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 00:35:07.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 00:35:07.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 00:35:07.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 00:35:07.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 00:35:07.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 00:35:07.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 00:35:07.394][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-07 00:35:07.414][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 00:35:07.416][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 00:35:07.419][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 00:35:07.421][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 00:35:07.430][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 00:35:07.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 00:35:07.434][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 00:35:07.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 00:35:07.444][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 00:35:07.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
>
> proc.time()
user system elapsed
40.133 2.075 99.945
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.685 | 1.209 | 7.479 | |
| ChebiEntry | 0.775 | 0.020 | 0.803 | |