Pierrick Roger
| Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-20 11:46 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2025-03-20 05:02:02 -0000 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 05:10:25 -0000 (Thu, 20 Mar 2025) |
| EllapsedTime: 503.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 1.166 0.044 5.484
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘biodbChebi’ ... ** this is package ‘biodbChebi’ version ‘1.13.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-20 05:03:02.755][biodb::testContext]
biodb.INFO [2025-03-20 05:03:02.758][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:03:02.759][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-20 05:03:02.761][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:03:02.762][biodb::testContext]
biodb.INFO [2025-03-20 05:03:02.771][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:03:02.774][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 05:03:02.783][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:03:02.785][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 05:03:02.786][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.792][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 05:03:02.820][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.825][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[2025-03-20 05:03:02.826][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 05:03:02.827][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.833][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 05:03:02.834][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 05:03:02.835][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 05:03:02.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.841][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 05:03:02.842][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 05:03:02.844][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.849][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 05:03:02.850][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 05:03:02.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.856][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 05:03:02.857][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 05:03:02.859][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 05:03:02.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.865][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 05:03:02.866][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.872][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 05:03:02.873][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 05:03:02.875][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 05:03:02.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.881][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:03:02.882][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 05:03:02.884][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 05:03:02.885][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 05:03:02.886][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 05:03:02.888][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 05:03:02.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.893][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 05:03:02.895][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 05:03:02.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.900][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 05:03:02.902][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 05:03:02.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.906][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[2025-03-20 05:03:02.907][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 05:03:02.909][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 05:03:02.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.914][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 05:03:02.915][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 05:03:02.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.919][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[2025-03-20 05:03:02.921][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 05:03:02.922][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 05:03:02.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.928][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:03:02.930][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 05:03:02.935][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 05:03:02.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.941][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 05:03:02.942][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 05:03:02.944][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 05:03:02.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:02.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:02.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:02.953][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 05:03:03.005][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.030][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 05:03:03.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:03:03.046][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.049][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.050][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.052][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:03:03.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:03:03.054][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 05:03:03.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:03:03.058][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.061][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:03:03.061][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:03:03.061][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:03:03.061][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:03:03.061][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:03:03.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:03:03.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:03:03.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.071][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:03:03.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:03:03.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.077][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.078][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 05:03:03.081][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.082][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:03:03.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:03:03.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.092][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:03:03.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:03:03.095][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.097][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 05:03:03.098][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:03:03.099][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.102][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:03:03.102][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:03:03.102][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:03:03.102][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:03:03.102][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:03:03.103][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:03:03.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.107][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:03:03.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.113][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.114][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:03:03.115][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:03:03.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.118][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.120][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 05:03:03.122][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.124][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 05:03:03.125][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:03:03.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.131][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.134][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:03:03.135][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:03:03.137][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.138][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 05:03:03.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:03:03.141][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.142][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.144][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.145][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:03:03.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:03:03.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.153][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.154][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.156][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:03:03.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:03:03.158][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.160][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 05:03:03.164][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:03:03.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:03:03.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.173][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.175][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:03:03.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:03:03.178][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.180][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 05:03:03.181][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:03:03.182][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.185][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.187][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:03:03.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:03:03.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.196][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:03:03.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:03:03.200][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.201][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:03:03.207][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:03:03.208][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.209][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[2025-03-20 05:03:03.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.273][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[2025-03-20 05:03:03.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.294][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[2025-03-20 05:03:03.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.312][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[2025-03-20 05:03:03.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.319][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 05:03:03.325][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 05:03:03.327][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 05:03:03.329][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 05:03:03.331][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:03:03.333][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 05:03:03.335][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 05:03:03.337][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 05:03:03.339][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 05:03:03.341][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 05:03:03.343][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:03:03.345][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 05:03:03.347][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 05:03:03.349][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 05:03:03.351][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 05:03:03.353][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 05:03:03.354][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 05:03:03.356][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 05:03:03.358][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:03:03.360][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 05:03:03.362][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 05:03:03.364][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 05:03:03.366][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 05:03:03.368][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 05:03:03.370][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 05:03:03.372][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 05:03:03.374][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 05:03:03.376][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 05:03:03.378][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 05:03:03.379][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 05:03:03.381][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 05:03:03.383][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 05:03:03.385][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 05:03:03.387][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 05:03:03.389][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 05:03:03.391][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 05:03:03.393][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 05:03:03.395][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 05:03:03.397][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 05:03:03.398][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 05:03:03.400][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 05:03:03.402][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 05:03:03.404][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 05:03:03.406][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 05:03:03.408][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 05:03:03.409][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 05:03:03.419][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 05:03:03.421][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 05:03:03.423][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 05:03:03.425][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 05:03:03.427][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 05:03:03.429][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 05:03:03.431][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 05:03:03.433][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 05:03:03.434][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 05:03:03.436][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 05:03:03.438][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 05:03:03.440][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 05:03:03.442][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 05:03:03.444][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 05:03:03.446][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 05:03:03.448][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 05:03:03.450][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 05:03:03.452][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 05:03:03.454][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 05:03:03.456][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 05:03:03.458][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:03:03.460][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:03:03.462][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 05:03:03.465][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 05:03:03.467][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 05:03:03.469][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 05:03:03.471][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 05:03:03.473][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 05:03:03.475][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 05:03:03.477][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 05:03:03.479][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 05:03:03.481][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 05:03:03.483][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 05:03:03.485][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 05:03:03.487][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 05:03:03.489][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 05:03:03.491][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 05:03:03.499][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 05:03:03.501][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:03:03.506][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:03:03.507][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.509][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.541][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[2025-03-20 05:03:03.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.549][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[2025-03-20 05:03:03.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.574][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[2025-03-20 05:03:03.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.641][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[2025-03-20 05:03:03.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.650][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[2025-03-20 05:03:03.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:03:03.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:03.660][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 05:03:03.674][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 05:03:03.677][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.678][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.679][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:03:03.682][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.683][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.685][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.686][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 05:03:03.687][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 05:03:03.689][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:03:03.690][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.691][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 05:03:03.692][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 05:03:03.694][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 05:03:03.695][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 05:03:03.697][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:03:03.697][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:03:03.697][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:03:03.698][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 05:03:03.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.702][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:03:03.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:03:03.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:03:03.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:03:03.707][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:03.707][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 05:03:03.708][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:03:03.709][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:03:03.710][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 05:03:03.712][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 05:03:03.712][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 05:03:03.720][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:03:03.723][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:03:03.725][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 05:03:03.727][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:03:03.729][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:03:03.731][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:03:03.762][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 05:03:03.764][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 05:03:03.769][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 05:03:03.775][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 05:03:03.791][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:03:03.793][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:03:03.794][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 05:03:03.796][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 05:03:03.808][biodb::testThat]
biodb.INFO [2025-03-20 05:03:03.809][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-20 05:03:03.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:03.812][biodb::testThat]
biodb.TRACE[2025-03-20 05:03:03.817][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-20 05:03:03.820][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:03.825][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:03.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:03.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:03.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:03.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:03.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:03.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:03.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:03.869][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:03.871][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:03.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.899][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:03.900][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:03.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.942][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:03.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:03.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.947][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:03.949][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:03.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.951][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:03.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:03.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.963][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:03.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:03.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.970][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:03.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:03.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:03.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:03.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.981][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:03.983][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:03.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.985][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:03.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.993][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:03.994][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:03.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:03.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:03.999][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:04.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.005][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.006][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.016][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.018][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.029][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:04.031][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.035][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:04.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.042][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.043][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:04.190][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-20 05:03:04.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.261][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:04.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:04.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:04.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:04.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:04.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:04.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.278][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:04.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:04.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.465][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.467][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:04.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.514][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.515][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.518][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.553][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.557][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.592][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.593][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.596][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.630][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.631][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.651][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.656][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.662][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.667][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.669][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.695][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.706][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.708][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.712][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.728][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.734][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.739][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.746][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.777][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.829][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.830][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.867][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.869][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.871][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.889][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:04.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:04.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.900][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:04.901][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:04.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.910][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:04.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:04.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.921][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:04.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:04.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:04.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.936][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.942][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.944][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:04.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.953][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:04.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.957][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:04.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.974][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.976][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:04.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.978][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.985][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:04.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:04.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:04.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:04.995][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:04.997][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:04.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.000][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 05:03:05.011][biodb::testThat]
biodb.INFO [2025-03-20 05:03:05.012][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-20 05:03:05.013][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:05.015][biodb::testThat]
biodb.DEBUG[2025-03-20 05:03:05.035][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-20 05:03:05.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:05.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-20 05:03:05.052][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:05.054][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-20 05:03:05.055][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:05.091][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:05.093][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:05.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:05.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:05.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:05.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:05.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:05.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:05.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:05.112][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.113][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.158][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:05.160][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:05.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.163][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.165][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:05.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:05.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.171][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:05.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:05.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:05.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:05.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.183][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:05.184][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:05.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:05.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:05.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:05.196][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:05.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:05.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:05.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.207][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:05.208][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:05.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.213][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:05.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:05.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.219][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:05.220][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:05.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.225][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:05.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:05.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.231][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:05.232][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:05.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.243][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.255][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:05.257][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:05.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.261][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:05.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:05.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.267][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:05.269][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:05.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:05.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:05.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:05.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:05.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:05.338][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-20 05:03:05.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-20 05:03:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-20 05:03:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-20 05:03:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-20 05:03:05.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-20 05:03:05.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-20 05:03:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:03:05.366][biodb::testThat]
biodb.INFO [2025-03-20 05:03:05.367][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-20 05:03:05.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:05.370][biodb::testThat]
biodb.TRACE[2025-03-20 05:03:05.374][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.375][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.378][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:05.380][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-20 05:03:05.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:05.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:05.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:05.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:05.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:05.437][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-20 05:03:05.443][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 05:03:05.481][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:05.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 05:03:05.506][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:05.508][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 05:03:05.543][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[2025-03-20 05:03:05.547][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:05.549][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:05.551][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:03:06.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:03:07.950][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:07.953][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 05:03:07.978][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 05:03:07.981][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-20 05:03:08.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:08.027][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:08.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.031][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.033][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.036][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 05:03:08.042][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.043][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-20 05:03:08.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:08.046][biodb::testThat]
biodb.TRACE[2025-03-20 05:03:08.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:08.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:08.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:08.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:08.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:08.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:08.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:08.185][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:08.190][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:08.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:03:08.194][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:08.196][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-20 05:03:08.219][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.221][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-20 05:03:08.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:08.224][biodb::testThat]
biodb.TRACE[2025-03-20 05:03:08.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:08.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:08.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:08.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:08.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:08.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:08.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:08.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:08.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:08.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:08.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.380][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 05:03:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 05:03:08.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:08.397][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 05:03:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:08.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:03:08.411][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.413][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-20 05:03:08.414][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:08.415][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.427][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.428][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-20 05:03:08.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:08.431][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.443][biodb::testThat]
biodb.INFO [2025-03-20 05:03:08.445][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-20 05:03:08.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:08.448][biodb::testThat]
biodb.DEBUG[2025-03-20 05:03:08.453][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-20 05:03:10.868][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-20 05:03:15.492][biodb::testThat]
biodb.INFO [2025-03-20 05:03:15.494][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-20 05:03:15.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:15.496][biodb::testThat]
biodb.DEBUG[2025-03-20 05:03:16.291][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[2025-03-20 05:03:18.095][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:18.096][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:18.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:18.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:18.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.105][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 05:03:18.107][biodb::testThat]
biodb.INFO [2025-03-20 05:03:18.109][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-20 05:03:18.110][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:03:18.111][biodb::testThat]
biodb.TRACE[2025-03-20 05:03:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:18.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:18.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:18.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:18.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:18.279][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:18.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:03:18.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:18.285][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 05:03:18.378][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:18.382][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:18.384][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:03:18.386][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:18.388][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-20 05:03:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 05:03:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 05:03:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:18.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:18.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:18.465][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:18.470][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:18.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 05:03:18.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:18.476][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 05:03:18.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:18.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:18.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:18.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:18.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:18.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:18.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:18.495][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-20 05:03:18.566][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:18.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-20 05:03:18.570][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:18.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:18.573][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:18.574][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:18.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:18.577][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:18.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:18.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:18.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:18.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:18.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:18.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:18.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:18.596][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-20 05:03:18.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:18.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:18.644][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-20 05:03:19.785][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-20 05:03:20.652][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:20.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-20 05:03:20.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-20 05:03:20.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-20 05:03:20.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:20.666][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:20.667][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:20.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:20.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:20.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:20.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:20.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:20.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:20.682][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[2025-03-20 05:03:20.686][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.687][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.709][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:20.711][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:20.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.715][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:20.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.720][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:20.722][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:20.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:20.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:20.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:20.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:20.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:20.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.743][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:20.745][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:20.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.747][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:20.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:20.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.754][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:20.756][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:20.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.760][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:20.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:20.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:20.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:20.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:20.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:20.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:20.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:20.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:20.795][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:20.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:20.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:20.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.804][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:20.806][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:20.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.810][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:20.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:20.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:20.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:20.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:20.869][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-20 05:03:20.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:20.901][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:20.906][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:20.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 05:03:20.909][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:20.912][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 05:03:20.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:20.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:20.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:20.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:20.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:20.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:20.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:20.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:20.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:20.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:20.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:20.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:20.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:20.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:20.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:20.986][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-20 05:03:20.988][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:20.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-20 05:03:20.992][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:20.993][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:20.994][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:20.996][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:20.997][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:20.998][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:21.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:21.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:21.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:21.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:21.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:21.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:21.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:21.033][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-20 05:03:21.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:21.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:21.040][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-20 05:03:21.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-20 05:03:23.774][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:23.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-20 05:03:23.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-20 05:03:23.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-20 05:03:23.787][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:23.789][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:23.791][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:23.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:23.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:23.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:23.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:23.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:23.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:23.806][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.TRACE[2025-03-20 05:03:23.809][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:23.811][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:23.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:23.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.820][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:23.822][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:23.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.826][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.832][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:23.833][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:23.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:23.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.843][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:23.844][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:23.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:23.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:23.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.854][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:23.856][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:23.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:23.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:23.868][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:23.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.872][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:23.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:23.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.878][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:23.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:23.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.913][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:23.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:23.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:23.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:23.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.927][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:23.928][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:23.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.934][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:23.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.940][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:23.942][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:23.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:23.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:23.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:23.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:23.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:23.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:23.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:23.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:24.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:24.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:24.045][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-20 05:03:24.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:24.094][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:03:24.100][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:03:24.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:03:24.104][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:03:24.106][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 05:03:24.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:24.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:24.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:24.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:24.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:24.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:24.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:24.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:24.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:24.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:24.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:24.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:24.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:24.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:24.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:24.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:24.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:24.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:24.162][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-20 05:03:24.164][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:24.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-20 05:03:24.168][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:24.170][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:24.171][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:24.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:24.175][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:24.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:24.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:24.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:24.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:24.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:24.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:24.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:24.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:24.196][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-20 05:03:24.200][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:24.201][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:24.204][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-20 05:03:26.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-20 05:03:28.317][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:28.321][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-20 05:03:28.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-20 05:03:28.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-20 05:03:28.332][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:28.334][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:28.335][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:28.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:28.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:28.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:28.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:28.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:28.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:28.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:28.354][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.356][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.366][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:28.368][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:28.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.386][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:28.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:28.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:28.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:28.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:28.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:28.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.403][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:28.405][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:28.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.409][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:28.411][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.415][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:28.416][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:28.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:28.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:28.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:28.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:28.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.432][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:28.434][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:28.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.438][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:28.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:28.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.444][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:28.445][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:28.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:28.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:28.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:28.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:28.504][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-20 05:03:28.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:28.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:28.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:28.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:28.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:28.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:28.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:28.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:28.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:28.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:28.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:28.547][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-20 05:03:28.549][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:28.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-20 05:03:28.553][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:28.554][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:28.556][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:28.557][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:28.558][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:28.560][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:28.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:28.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:28.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:28.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:28.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:28.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:28.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:28.578][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-20 05:03:28.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:28.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:28.585][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-20 05:03:29.681][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-20 05:03:30.674][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:30.677][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-20 05:03:30.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-20 05:03:30.685][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-20 05:03:30.687][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:30.688][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:30.690][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:30.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:30.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:30.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:30.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:30.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:30.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:30.705][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.TRACE[2025-03-20 05:03:30.708][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.734][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:30.736][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:30.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.740][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:30.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:30.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:30.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:30.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.753][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:30.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:30.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.759][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:30.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:30.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.766][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:30.767][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.770][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:30.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:30.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.778][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:30.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:30.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:30.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:30.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.791][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:30.792][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:30.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.797][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:30.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:30.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.802][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:30.804][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:30.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:30.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:30.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:30.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:30.865][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-20 05:03:30.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:30.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:30.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:30.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:30.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:30.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:30.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:30.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:30.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:30.910][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-20 05:03:30.912][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:30.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-20 05:03:30.916][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:30.918][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:30.919][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:30.921][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:30.922][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:30.924][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:30.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:30.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:30.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:30.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:30.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:30.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:30.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:30.943][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-20 05:03:30.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:30.949][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:30.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-20 05:03:35.004][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-20 05:03:35.790][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:35.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-20 05:03:35.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-20 05:03:35.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-20 05:03:35.818][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:35.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:35.826][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:35.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:35.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:35.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:35.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:35.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:35.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:35.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:35.874][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:35.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:35.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:35.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:35.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.892][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:35.917][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:35.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.950][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:35.952][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:35.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:35.968][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:35.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.982][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:35.984][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:35.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:35.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:35.997][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:35.999][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:36.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.012][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:36.014][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:36.029][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:36.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.039][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:36.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:36.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:36.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:36.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.071][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:36.072][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:36.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.077][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:36.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:36.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.083][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:36.085][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:36.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:36.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:36.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:36.148][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-20 05:03:36.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:36.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:36.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:36.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:36.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:36.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:36.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:36.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:36.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:36.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:36.197][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-20 05:03:36.199][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:36.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-20 05:03:36.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:36.205][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:36.207][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:36.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:36.210][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:36.212][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:36.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:36.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:36.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:36.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:36.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:36.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:36.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:36.235][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-20 05:03:36.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:36.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:36.243][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-20 05:03:37.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-20 05:03:39.395][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:39.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-20 05:03:39.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-20 05:03:39.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-20 05:03:39.423][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:39.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:39.431][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:39.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:39.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:39.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:39.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:39.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:39.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:39.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:39.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.548][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:39.550][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:39.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:39.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:39.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.575][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:39.581][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:39.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:39.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:39.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:39.608][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:39.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:39.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:39.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:39.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:39.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.662][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:39.664][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:39.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.677][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:39.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.688][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:39.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.703][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:39.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:39.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:39.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:39.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:39.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.749][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:39.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:39.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:39.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:39.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.781][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:39.783][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:39.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.796][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:39.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:39.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.808][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:39.814][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:39.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.823][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:39.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:39.974][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-20 05:03:39.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:39.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:39.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:40.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:40.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:40.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:40.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:40.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:40.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:40.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:40.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:40.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:40.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:40.054][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-20 05:03:40.055][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:40.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-20 05:03:40.068][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:40.070][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:40.076][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:40.078][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:40.080][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:40.086][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:40.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:40.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:40.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:40.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:40.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:40.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:40.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:40.149][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-20 05:03:40.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:40.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:40.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-20 05:03:41.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-20 05:03:42.198][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:42.205][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-20 05:03:42.215][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-20 05:03:42.223][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-20 05:03:42.230][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:42.236][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:42.238][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:42.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:42.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:42.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:42.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:42.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:42.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:42.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:42.285][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.287][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.311][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:42.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:42.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:42.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.342][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:42.349][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:42.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:42.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:42.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.375][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:42.381][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:42.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:42.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:42.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:42.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:42.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.421][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:42.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:42.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:42.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:42.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.463][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:42.469][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.493][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:42.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:42.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:42.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:42.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.518][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:42.520][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:42.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:42.550][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:42.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.557][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.573][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:42.575][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:42.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:42.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:42.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:42.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:42.737][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-20 05:03:42.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:42.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:42.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:42.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:42.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:42.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:42.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:42.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:42.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:42.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:42.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:42.840][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-20 05:03:42.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:42.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-20 05:03:42.851][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:42.857][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:42.858][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:42.864][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:42.866][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:42.867][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:42.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:42.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:42.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:42.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:42.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:42.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:42.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:42.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-20 05:03:42.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:42.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:42.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-20 05:03:43.774][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-20 05:03:44.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:44.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-20 05:03:44.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-20 05:03:44.568][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-20 05:03:44.574][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:44.581][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:44.583][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:44.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:44.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:44.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:44.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:44.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:44.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:44.629][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.TRACE[2025-03-20 05:03:44.638][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:44.640][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:44.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:44.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:44.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.670][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:44.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:44.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.686][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:44.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:44.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.702][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:44.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:44.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:44.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.734][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:44.736][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:44.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:44.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:44.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.765][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:44.767][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:44.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:44.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.796][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:44.798][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:44.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:44.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:44.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.828][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:44.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:44.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:44.846][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:44.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:44.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:44.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.872][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:44.878][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:44.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:44.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:44.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.904][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:44.910][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:44.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.918][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.920][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:44.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.935][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:44.942][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:44.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.950][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:44.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:44.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:44.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:44.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:44.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:44.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:45.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:45.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:45.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:45.181][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-20 05:03:45.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:45.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:45.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:45.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:45.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:45.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:45.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:45.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:45.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:45.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:45.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:45.270][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-20 05:03:45.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:45.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-20 05:03:45.285][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:45.287][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:45.293][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:45.295][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:45.301][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:45.303][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:45.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:45.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:45.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:45.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:45.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:45.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:45.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:45.350][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-20 05:03:45.359][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:45.365][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:45.367][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-20 05:03:47.751][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-20 05:03:49.762][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-20 05:03:49.765][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-20 05:03:49.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-20 05:03:49.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-20 05:03:49.786][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-20 05:03:49.788][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:49.790][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:49.792][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:49.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:49.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:49.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:49.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:49.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:49.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:49.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:49.829][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:49.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:49.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:49.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:49.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.855][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:49.860][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:49.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.869][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:49.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.880][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:49.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:49.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:49.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:49.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.918][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:49.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:49.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:49.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.944][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:49.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:49.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.950][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:49.951][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:49.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:49.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:49.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:49.963][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:49.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.966][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:49.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.973][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:49.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:49.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:49.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.985][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:49.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:49.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:49.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:49.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:49.997][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:50.011][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:50.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.016][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:50.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:50.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:50.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:50.080][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-20 05:03:50.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:50.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:50.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:50.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:50.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:50.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:50.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:50.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:50.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:50.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:50.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:50.113][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-20 05:03:50.114][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:50.116][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-20 05:03:50.118][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:50.120][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:50.121][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:50.123][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:50.124][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:50.125][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:50.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:50.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:50.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:50.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:50.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:50.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:50.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:50.144][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-20 05:03:50.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:50.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:50.152][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-20 05:03:51.356][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-20 05:03:52.113][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-20 05:03:52.115][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-20 05:03:52.118][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-20 05:03:52.123][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-20 05:03:52.131][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-20 05:03:52.133][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:52.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:52.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:52.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:52.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:52.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:52.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:52.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:52.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:52.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:52.155][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.157][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.160][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.167][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:52.171][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:52.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.176][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:52.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:52.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:52.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:52.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.197][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:52.199][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:52.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:52.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:52.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.209][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:52.211][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:52.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.214][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:52.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:52.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.221][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:52.223][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:52.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.228][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:52.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.234][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:52.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:52.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.256][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:52.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:52.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.264][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:52.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:52.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:52.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:52.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:52.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:52.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.283][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:52.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:52.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.289][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:52.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:52.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.295][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:52.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:52.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:52.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:52.373][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-20 05:03:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:52.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:52.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:52.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:52.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:52.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:52.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:52.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:52.413][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-20 05:03:52.415][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:52.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-20 05:03:52.420][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:52.422][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:52.423][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:52.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:52.427][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:52.428][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:52.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:52.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:52.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:52.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:52.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:52.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:52.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:52.450][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-20 05:03:52.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:52.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:52.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-20 05:03:54.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-20 05:03:55.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:55.019][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-20 05:03:55.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-20 05:03:55.071][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-20 05:03:55.086][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:55.097][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:55.099][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:55.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:55.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:55.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:55.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:55.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:55.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:55.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:03:55.192][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.228][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:55.230][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:55.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.240][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:55.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:55.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.247][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:55.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:55.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:55.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:55.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.336][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:55.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:55.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.341][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:55.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:55.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:55.352][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:55.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:55.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:55.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.364][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:55.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:55.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.373][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:55.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.378][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.379][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:55.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.386][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:55.388][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:55.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.399][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:55.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:55.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:55.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:55.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.412][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:55.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:55.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:55.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:55.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.425][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:55.427][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:55.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:55.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:55.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:55.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:55.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:55.500][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-20 05:03:55.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:55.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:55.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:55.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:55.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:55.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:55.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:55.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:55.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:55.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:55.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:55.533][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-20 05:03:55.535][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:55.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-20 05:03:55.539][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:55.540][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:55.542][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:55.544][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:55.545][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:55.546][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:55.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:55.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:55.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:55.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:55.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:55.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:55.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:55.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-20 05:03:55.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:55.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:55.573][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-20 05:03:56.353][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-20 05:03:57.118][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:03:57.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-20 05:03:57.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-20 05:03:57.138][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-20 05:03:57.145][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:03:57.147][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:03:57.153][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:03:57.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:57.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:57.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:57.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:57.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:57.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:57.220][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[2025-03-20 05:03:57.228][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.234][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.241][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.259][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:57.265][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:57.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.275][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:03:57.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:03:57.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.290][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:57.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:57.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:03:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:03:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:57.323][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:57.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:03:57.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:03:57.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:57.354][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:57.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:03:57.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:03:57.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.378][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:57.384][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:03:57.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.394][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:57.396][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.410][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:03:57.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.426][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:57.427][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:57.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:03:57.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.457][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:57.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:57.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:03:57.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:03:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.488][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:57.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:57.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.500][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:03:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:03:57.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:57.521][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:57.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:03:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:03:57.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:03:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:03:57.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:03:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:57.691][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-20 05:03:57.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:03:57.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:03:57.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:03:57.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:03:57.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:57.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:57.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:57.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:57.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:57.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:57.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:57.771][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-20 05:03:57.777][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:03:57.779][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-20 05:03:57.786][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:03:57.792][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:03:57.794][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:03:57.796][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:03:57.797][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:03:57.799][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:03:57.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:03:57.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:03:57.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:03:57.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:03:57.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:03:57.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:03:57.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:03:57.839][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-20 05:03:57.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:03:57.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:03:57.872][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-20 05:04:00.643][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-20 05:04:01.476][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:01.481][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-20 05:04:01.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-20 05:04:01.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-20 05:04:01.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:01.508][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:01.511][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:01.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:01.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:01.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:01.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:01.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:01.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:01.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:01.565][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.567][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.600][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:01.602][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:01.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.612][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:01.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:01.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.627][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:01.633][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:01.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:01.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.658][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:01.660][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:01.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.673][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:01.675][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:01.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.683][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:01.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:01.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.704][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:01.706][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:01.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.731][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:01.737][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:01.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:01.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:01.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.761][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:01.762][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:01.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.770][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:01.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:01.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.787][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:01.793][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:01.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:01.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.817][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:01.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:01.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:01.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:01.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:01.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:01.964][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-20 05:04:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:01.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:01.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:01.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:02.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:02.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:02.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:02.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:02.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:02.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:02.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:02.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:02.044][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-20 05:04:02.046][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:02.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-20 05:04:02.055][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:02.062][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:02.063][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:02.069][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:02.071][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:02.077][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:02.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:02.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:02.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:02.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:02.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:02.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:02.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:02.160][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-20 05:04:02.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:02.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:02.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-20 05:04:02.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-20 05:04:03.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:03.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-20 05:04:03.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-20 05:04:03.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-20 05:04:03.760][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:03.762][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:03.764][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:03.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:03.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:03.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:03.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:03.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:03.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:03.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:03.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:03.838][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:03.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:03.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.874][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:03.875][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:03.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:03.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.899][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:03.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:03.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:03.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.929][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:03.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:03.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:03.946][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:03.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:03.961][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:03.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.971][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:03.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:03.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:03.986][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:03.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:03.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:03.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.001][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:04.003][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:04.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:04.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:04.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.027][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:04.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:04.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:04.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:04.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.058][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:04.060][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:04.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.073][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:04.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:04.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.088][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:04.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:04.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:04.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:04.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:04.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:04.243][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-20 05:04:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:04.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:04.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:04.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:04.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:04.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:04.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:04.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:04.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:04.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:04.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:04.354][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-20 05:04:04.360][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:04.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-20 05:04:04.369][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:04.371][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:04.376][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:04.378][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:04.380][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:04.385][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:04.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:04.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:04.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:04.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:04.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:04.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:04.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:04.426][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-20 05:04:04.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:04.440][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:04.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-20 05:04:05.230][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-20 05:04:06.018][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:06.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-20 05:04:06.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-20 05:04:06.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-20 05:04:06.064][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:06.066][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:06.076][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:06.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:06.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:06.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:06.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:06.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:06.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:06.125][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[2025-03-20 05:04:06.133][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.134][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.159][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:06.165][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:06.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.175][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:06.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.190][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:06.192][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:06.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:06.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:06.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.220][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:06.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:06.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:06.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.247][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:06.252][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:06.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:06.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:06.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.277][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:06.279][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:06.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.288][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:06.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.318][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:06.320][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:06.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:06.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.348][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:06.350][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:06.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:06.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:06.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:06.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:06.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.384][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.390][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:06.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.405][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:06.407][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:06.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:06.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:06.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:06.654][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-20 05:04:06.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:06.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:06.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:06.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:06.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:06.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:06.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:06.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:06.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:06.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:06.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:06.751][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-20 05:04:06.757][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:06.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-20 05:04:06.767][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:06.773][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:06.775][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:06.781][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:06.783][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:06.789][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:06.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:06.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:06.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:06.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:06.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:06.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:06.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:06.837][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-20 05:04:06.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:06.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:06.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-20 05:04:07.677][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-20 05:04:08.438][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:08.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-20 05:04:08.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-20 05:04:08.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-20 05:04:08.463][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:08.469][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:08.471][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:08.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:08.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:08.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:08.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:08.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:08.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:08.494][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.TRACE[2025-03-20 05:04:08.499][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.500][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.511][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:08.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:08.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:08.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.524][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:08.526][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:08.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.537][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:08.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:08.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.549][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:08.551][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:08.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:08.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.562][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:08.564][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:08.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.569][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:08.571][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:08.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.581][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:08.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:08.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:08.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:08.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.594][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:08.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:08.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:08.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.606][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:08.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:08.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.613][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:08.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.619][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:08.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:08.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.624][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:08.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:08.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:08.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:08.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:08.753][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-20 05:04:08.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:08.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:08.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:08.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:08.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:08.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:08.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:08.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:08.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:08.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:08.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:08.819][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-20 05:04:08.820][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:08.827][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-20 05:04:08.832][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:08.834][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:08.836][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:08.841][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:08.843][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:08.844][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:08.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:08.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:08.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:08.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:08.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:08.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:08.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:08.883][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-20 05:04:08.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:08.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:08.899][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-20 05:04:09.674][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-20 05:04:10.473][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:10.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-20 05:04:10.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-20 05:04:10.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-20 05:04:10.489][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:10.491][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:10.494][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:10.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:10.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:10.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:10.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:10.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:10.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:10.512][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[2025-03-20 05:04:10.515][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.516][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.527][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:10.528][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:10.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.533][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:10.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:10.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.539][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:10.541][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:10.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.546][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:10.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:10.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.552][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:10.553][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:10.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:10.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:10.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:10.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:10.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.576][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:10.578][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:10.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.582][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:10.584][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.587][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:10.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:10.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:10.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.607][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:10.608][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:10.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:10.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:10.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.619][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:10.634][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:10.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.637][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.639][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:10.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:10.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.646][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:10.647][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:10.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:10.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:10.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:10.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:10.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:10.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:10.717][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-20 05:04:10.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:10.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:10.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:10.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:10.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:10.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:10.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:10.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:10.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:10.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:10.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:10.751][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-20 05:04:10.753][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:10.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-20 05:04:10.757][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:10.759][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:10.760][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:10.762][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:10.764][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:10.765][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:10.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:10.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:10.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:10.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:10.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:10.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:10.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:10.784][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-20 05:04:10.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:10.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:10.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-20 05:04:11.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-20 05:04:12.514][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:12.521][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-20 05:04:12.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-20 05:04:12.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-20 05:04:12.557][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:12.559][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:12.569][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:12.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:12.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:12.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:12.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:12.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:12.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:12.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:12.629][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:12.631][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:12.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:12.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:12.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.667][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:12.676][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:12.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:12.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:12.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.712][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:12.714][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:12.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:12.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:12.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.750][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:12.751][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:12.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.783][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:12.789][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:12.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:12.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:12.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.813][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:12.815][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:12.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.872][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:12.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:12.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:12.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.912][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:12.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:12.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:12.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.949][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:12.951][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:12.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.982][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:12.989][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:12.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:12.996][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:12.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:13.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:13.021][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:13.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:13.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:13.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:13.167][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-20 05:04:13.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:13.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:13.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:13.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:13.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:13.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:13.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:13.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:13.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:13.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:13.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:13.204][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-20 05:04:13.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:13.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-20 05:04:13.211][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:13.212][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:13.214][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:13.216][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:13.217][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:13.219][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:13.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:13.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:13.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:13.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:13.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:13.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:13.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:13.240][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-20 05:04:13.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:13.246][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:13.249][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-20 05:04:14.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-20 05:04:16.506][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:16.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-20 05:04:16.535][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-20 05:04:16.552][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-20 05:04:16.559][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:16.569][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:16.571][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:16.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:16.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:16.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:16.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:16.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:16.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:16.630][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.TRACE[2025-03-20 05:04:16.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.653][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.691][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:16.701][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:16.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.715][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:16.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:16.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.730][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:16.732][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:16.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:16.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.805][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:16.807][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:16.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.814][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:16.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:16.845][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:16.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:16.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:16.871][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:16.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.876][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:16.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:16.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:16.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.888][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:16.889][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:16.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:16.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:16.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.900][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:16.901][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:16.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:16.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:16.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.911][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:16.913][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:16.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.917][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:16.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:16.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.923][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:16.925][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:16.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.929][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:16.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:16.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:16.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:16.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:16.992][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-20 05:04:16.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:16.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:16.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:16.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:17.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:17.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:17.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:17.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:17.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:17.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:17.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:17.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:17.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:17.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:17.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:17.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:17.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:17.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:17.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:17.026][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-20 05:04:17.027][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:17.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-20 05:04:17.032][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:17.033][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:17.035][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:17.036][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:17.038][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:17.039][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:17.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:17.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:17.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:17.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:17.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:17.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:17.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:17.058][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-20 05:04:17.062][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:17.064][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:17.066][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-20 05:04:17.958][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-20 05:04:18.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:18.826][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-20 05:04:18.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-20 05:04:18.844][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-20 05:04:18.850][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:18.857][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:18.858][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:18.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:18.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:18.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:18.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:18.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:18.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:18.939][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[2025-03-20 05:04:18.946][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:18.948][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:18.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:18.955][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:18.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:18.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:18.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:18.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:18.986][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:18.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:18.993][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:18.995][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:19.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.021][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:19.022][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:19.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:19.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:19.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.047][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:19.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:19.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:19.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:19.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.077][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:19.079][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:19.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:19.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:19.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.103][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:19.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:19.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.119][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:19.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.134][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:19.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.149][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:19.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:19.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:19.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:19.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.175][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:19.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:19.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.184][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:19.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.206][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:19.207][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:19.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.221][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.236][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:19.238][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:19.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:19.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:19.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:19.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:19.399][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-20 05:04:19.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:19.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:19.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:19.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:19.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:19.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:19.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:19.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:19.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:19.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:19.477][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-20 05:04:19.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:19.485][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-20 05:04:19.492][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:19.494][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:19.496][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:19.502][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:19.503][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:19.509][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:19.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:19.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:19.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:19.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:19.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:19.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:19.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:19.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-20 05:04:19.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:19.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:19.586][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-20 05:04:30.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-20 05:04:31.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:31.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-20 05:04:31.336][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-20 05:04:31.352][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-20 05:04:31.358][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:04:31.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:04:31.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:04:31.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:31.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:31.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:31.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:31.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:31.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:31.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:31.495][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.497][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.528][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:31.530][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:31.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.536][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:04:31.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:04:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.543][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:31.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:31.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:04:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:04:31.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.560][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:31.562][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:31.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:04:31.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:04:31.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:31.576][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:31.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:04:31.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:04:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:31.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:04:31.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.599][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:31.601][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.608][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:04:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.615][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:31.617][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:31.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:31.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:31.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.636][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:31.638][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:31.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:04:31.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:04:31.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.652][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:31.653][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:31.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.659][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:04:31.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:04:31.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.666][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:31.668][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:31.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:04:31.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:04:31.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:04:31.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:04:31.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:04:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:31.759][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-20 05:04:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:31.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:31.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:31.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:31.865][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:04:31.872][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:31.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:31.881][private$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[2025-03-20 05:04:40.628][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[2025-03-20 05:04:43.611][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:43.728][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 05:04:43.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 05:04:44.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:44.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:44.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:44.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.087][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[2025-03-20 05:04:45.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.220][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[2025-03-20 05:04:45.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.269][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.TRACE[2025-03-20 05:04:45.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.366][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[2025-03-20 05:04:45.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.402][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.TRACE[2025-03-20 05:04:45.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.541][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[2025-03-20 05:04:45.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.804][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[2025-03-20 05:04:45.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:45.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:45.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:45.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:45.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:45.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:45.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:45.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:04:45.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:04:45.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:45.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:47.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:47.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:47.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:47.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:47.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:47.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:04:47.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:04:47.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:04:47.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:04:47.736][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[2025-03-20 05:04:47.781][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:47.783][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:47.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:04:48.602][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:04:53.864][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:53.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-20 05:04:53.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-20 05:04:53.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:04:53.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:54.001][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:54.007][private$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[2025-03-20 05:04:55.088][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[2025-03-20 05:04:57.852][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:04:57.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-20 05:04:57.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-20 05:04:57.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:57.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:57.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:57.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:57.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:57.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:57.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:57.899][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-20 05:04:57.900][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:04:57.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-20 05:04:57.905][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:04:57.906][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:04:57.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:04:57.910][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:04:57.911][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:04:57.913][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:04:57.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:04:57.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:04:57.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:04:57.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:04:57.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:04:57.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:04:57.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:04:57.933][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-20 05:04:57.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:04:57.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:04:57.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-20 05:04:58.754][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-20 05:05:06.963][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:05:06.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-20 05:05:06.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-20 05:05:07.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-20 05:05:07.002][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:05:07.008][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:05:07.010][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:05:07.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:05:07.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:05:07.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:05:07.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:05:07.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:05:07.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:05:07.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:05:07.078][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.080][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.093][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:05:07.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:05:07.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.100][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:05:07.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:05:07.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.107][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:05:07.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:05:07.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.115][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:05:07.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:05:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.123][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:05:07.124][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:05:07.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:05:07.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:05:07.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:05:07.138][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:05:07.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:05:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:05:07.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.226][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:05:07.228][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:05:07.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.233][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:05:07.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:05:07.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.239][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:05:07.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:05:07.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.246][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:05:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:05:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.265][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:05:07.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:05:07.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.269][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:05:07.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:05:07.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:05:07.279][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:05:07.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.284][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:05:07.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:05:07.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:05:07.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:05:07.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.296][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:05:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:05:07.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:05:07.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:05:07.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:05:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:05:07.363][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-20 05:05:07.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:05:07.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:05:07.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:05:07.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:05:07.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:05:07.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:05:07.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:05:07.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:05:07.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:05:07.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:05:07.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:05:07.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:05:07.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:05:07.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:05:07.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:05:07.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:05:07.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:05:07.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:05:07.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:05:07.479][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-20 05:05:07.480][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:05:07.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-20 05:05:07.484][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:05:07.486][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:05:07.488][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:05:07.489][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:05:07.491][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:05:07.492][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:05:07.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:05:07.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:05:07.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:05:07.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:05:07.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:05:07.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:05:07.512][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[2025-03-20 05:05:07.513][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-20 05:05:07.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:05:07.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:05:07.521][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-20 05:06:21.708][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447 does not exist.
biodb.TRACE[2025-03-20 05:06:21.714][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-20 05:06:21.716][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-20 05:06:21.718][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-20 05:06:23.011][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:06:26.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-20 05:06:26.795][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-20 05:06:26.807][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-20 05:06:26.814][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:06:26.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:06:26.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:06:26.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:26.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:26.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:26.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:26.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:26.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:26.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:26.915][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:26.917][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:26.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.920][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:26.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.929][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:06:26.931][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:06:26.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.936][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:06:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:06:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.943][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:06:26.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:06:26.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:06:26.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:06:26.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.957][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:06:26.958][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:06:26.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:06:26.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:06:26.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:06:26.973][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:06:26.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.976][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:06:26.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:06:26.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:26.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:06:26.987][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:06:26.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:26.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.001][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:06:27.017][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:06:27.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:06:27.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:06:27.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.042][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.048][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.073][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:06:27.075][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:06:27.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:06:27.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:06:27.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.105][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:06:27.106][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:06:27.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.116][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:06:27.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:06:27.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.131][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:06:27.137][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:06:27.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.145][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:06:27.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:06:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:06:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:06:27.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:06:27.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:27.258][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-20 05:06:27.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:27.342][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[2025-03-20 05:06:27.381][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:06:27.384][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:06:27.390][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:06:27.453][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 05:06:27.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:27.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:27.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:27.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:27.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:27.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:27.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:27.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:27.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:27.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:27.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:27.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:27.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:27.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:27.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:27.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:27.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:27.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:27.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:27.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:27.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:27.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:27.692][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[2025-03-20 05:06:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:27.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:27.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:27.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:27.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:27.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:29.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:29.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:29.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:29.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:29.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:29.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:29.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:29.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:29.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:29.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:29.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:29.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:29.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:29.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:29.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:29.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:31.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:31.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:31.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:31.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:31.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:31.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:31.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:31.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:31.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:31.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:31.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:31.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:31.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:31.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:31.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:31.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:31.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:31.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:31.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:31.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:31.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:31.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:31.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:31.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:31.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:31.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:31.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:31.997][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.TRACE[2025-03-20 05:06:31.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:32.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:32.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:32.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:32.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:32.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:32.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:32.032][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[2025-03-20 05:06:32.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:32.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:32.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:32.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:32.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:32.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:32.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:32.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:32.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:32.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:32.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:32.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:37.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:37.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:37.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:37.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:37.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:37.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:37.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:37.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:37.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:37.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:38.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:38.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:38.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:38.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:38.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:38.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:38.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:38.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:38.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:38.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:38.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:38.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:38.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:38.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:38.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:38.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:38.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:38.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:38.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:38.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:38.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:38.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:38.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:38.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:38.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:38.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:38.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:38.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:38.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:38.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:38.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:38.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:38.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:38.197][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[2025-03-20 05:06:38.226][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:06:38.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 05:06:38.230][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:06:38.265][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 05:06:49.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:50.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:50.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:56.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:56.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:56.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:56.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:56.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:56.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:56.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:56.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:56.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:56.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:56.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:56.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:56.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:56.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:56.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:56.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:56.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:59.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:59.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:59.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:59.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:59.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:59.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:59.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:59.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:59.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:59.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:59.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:59.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:59.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:59.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:59.793][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.TRACE[2025-03-20 05:06:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:59.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:59.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:59.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:59.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:59.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:59.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:59.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:59.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:59.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:59.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:59.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:59.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:06:59.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:06:59.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:06:59.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:06:59.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:06:59.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:06:59.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:06:59.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:06:59.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:06:59.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:06:59.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:06:59.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:00.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:00.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:00.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:00.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:00.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:00.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:00.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:00.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:00.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:00.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:00.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:00.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:00.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:00.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:00.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:00.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:00.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:00.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:00.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:00.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:00.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:00.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:00.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:00.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:00.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:00.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:00.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:00.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:00.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:00.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:01.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:01.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:01.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:01.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:01.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:01.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:01.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:01.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:01.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:01.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:02.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:02.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:02.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:02.030][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[2025-03-20 05:07:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:02.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:02.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:02.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:02.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:02.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:02.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:02.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:02.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:02.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:02.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:02.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:02.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:02.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:02.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:02.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:07:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:07:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.218][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 05:07:02.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 05:07:02.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:07:02.239][biodb::testThat]
biodb.INFO [2025-03-20 05:07:02.242][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-20 05:07:02.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:07:02.247][biodb::testThat]
biodb.TRACE[2025-03-20 05:07:02.357][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 05:07:02.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 05:07:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:07:02.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:07:02.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:07:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:07:02.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:07:02.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:07:02.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:07:02.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:07:02.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:07:02.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:07:02.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:07:02.524][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[2025-03-20 05:07:02.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:07:02.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:07:02.595][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:08:10.681][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-03-20 05:08:10.701][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-20 05:08:10.705][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-20 05:08:10.708][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:08:43.688][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:08:43.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-20 05:08:43.841][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-20 05:08:43.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:08:43.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:08:43.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:08:43.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:08:43.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:08:43.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:08:43.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:08:43.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:08:43.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:08:43.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:08:43.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:08:43.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:08:43.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:08:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:08:44.005][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:08:44.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:08:44.103][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:08:44.106][private$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[2025-03-20 05:08:50.230][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[2025-03-20 05:09:00.940][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:12.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-20 05:09:12.799][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-20 05:09:12.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:12.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:12.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:12.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:12.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:12.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:12.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:12.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:12.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:12.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:12.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:12.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:12.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:12.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:12.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:12.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:12.964][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:12.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:12.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:12.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:12.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:12.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:12.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:12.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:12.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:12.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:12.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:12.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:12.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:12.998][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:12.999][private$selectFields]
biodb.TRACE[2025-03-20 05:09:13.001][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:13.002][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:13.004][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:13.005][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.017][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.019][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:13.020][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:13.022][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.028][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:13.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 05:09:13.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:13.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:13.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:13.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:13.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:13.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:13.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:13.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:13.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:13.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:13.107][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:13.118][private$selectFields]
biodb.TRACE[2025-03-20 05:09:16.702][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:16.705][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:16.708][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:16.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.721][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:16.728][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:16.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.732][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.737][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:16.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:16.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:16.768][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:16.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:16.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:16.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:16.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:16.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:16.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:16.811][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.TRACE[2025-03-20 05:09:16.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:39.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.680][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:42.682][private$selectFields]
biodb.TRACE[2025-03-20 05:09:42.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:42.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:42.687][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:42.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.695][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.702][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:42.704][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:42.705][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.712][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:42.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:42.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.736][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 05:09:42.738][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:42.739][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:42.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:42.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:42.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:42.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:43.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:43.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:43.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:43.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:43.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:43.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:43.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:43.067][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[2025-03-20 05:09:43.133][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:43.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:43.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:09:44.548][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:09:45.312][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:45.320][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-20 05:09:45.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-20 05:09:45.340][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:09:45.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:45.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:45.349][private$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[2025-03-20 05:09:46.172][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[2025-03-20 05:09:46.952][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:46.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-20 05:09:46.961][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-20 05:09:46.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:46.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:46.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:46.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:46.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:46.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:46.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:46.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:46.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:46.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:46.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:46.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:46.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:46.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:46.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.012][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[2025-03-20 05:09:47.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.045][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[2025-03-20 05:09:47.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:47.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.099][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:47.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.189][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.191][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.193][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.194][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.200][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.211][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.213][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.222][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.247][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 05:09:47.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.350][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.352][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.353][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.364][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.390][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.394][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.399][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.422][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:47.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.459][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.TRACE[2025-03-20 05:09:47.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.479][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.481][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.486][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.492][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.508][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.528][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 05:09:47.529][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:47.531][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:47.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:47.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:09:47.554][biodb::testThat]
biodb.INFO [2025-03-20 05:09:47.555][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-20 05:09:47.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:47.558][biodb::testThat]
biodb.TRACE[2025-03-20 05:09:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 05:09:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 05:09:47.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.610][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[2025-03-20 05:09:47.614][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[2025-03-20 05:09:47.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:47.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 05:09:47.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:47.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 05:09:47.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.664][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[2025-03-20 05:09:47.669][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:47.671][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 05:09:47.673][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:47.675][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 05:09:47.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.692][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[2025-03-20 05:09:47.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:47.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:47.754][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:47.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.783][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.784][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.785][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.787][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.788][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.790][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.791][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.794][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.801][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.802][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.805][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.809][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.828][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 05:09:47.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.856][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.858][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.859][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.860][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.863][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.865][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.869][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.876][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.878][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.879][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.883][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.903][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:47.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:47.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:47.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:47.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:47.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:47.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:47.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:47.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.931][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.933][private$selectFields]
biodb.TRACE[2025-03-20 05:09:47.934][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:47.936][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:47.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.945][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.946][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.951][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.952][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:47.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.960][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:47.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:47.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:47.980][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 05:09:47.981][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:47.982][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:48.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.045][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.DEBUG[2025-03-20 05:09:48.049][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[2025-03-20 05:09:48.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 05:09:48.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.060][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 05:09:48.064][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[2025-03-20 05:09:48.069][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 05:09:48.072][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.074][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 05:09:48.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.125][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[2025-03-20 05:09:48.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.183][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:48.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.212][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.213][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.215][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.216][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.217][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.220][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.231][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.238][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.257][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 05:09:48.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.294][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.295][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.296][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.312][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.317][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.318][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.337][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:48.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.363][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.365][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.366][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.367][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.369][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.370][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.371][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.377][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.382][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.385][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.390][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.409][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 05:09:48.410][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:48.412][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:48.423][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:48.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:48.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:09:48.433][biodb::testThat]
biodb.INFO [2025-03-20 05:09:48.435][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-20 05:09:48.436][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:48.437][biodb::testThat]
biodb.TRACE[2025-03-20 05:09:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 05:09:48.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 05:09:48.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:48.492][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[2025-03-20 05:09:48.496][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.498][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 05:09:48.500][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.502][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 05:09:48.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.547][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[2025-03-20 05:09:48.551][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.553][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 05:09:48.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.557][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 05:09:48.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:48.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.624][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:48.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.652][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.654][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.655][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.656][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.659][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.664][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.665][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.670][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.671][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.673][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.678][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.680][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.699][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 05:09:48.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.728][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.730][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.731][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.734][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.735][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.746][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.748][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.749][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.753][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.772][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:48.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.808][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.810][private$selectFields]
biodb.TRACE[2025-03-20 05:09:48.811][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:48.813][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:48.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.815][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.817][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.825][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.828][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:48.829][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.835][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:48.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:48.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.853][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 05:09:48.855][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:48.856][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:48.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:48.926][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[2025-03-20 05:09:48.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 05:09:48.934][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.936][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 05:09:48.941][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[2025-03-20 05:09:48.945][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:09:48.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 05:09:48.949][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:09:48.951][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 05:09:48.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:48.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:48.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:48.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:48.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:48.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:48.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:48.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:48.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:48.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:48.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:48.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:49.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:49.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:49.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:49.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:49.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:49.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:49.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:49.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:49.063][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 05:09:49.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:49.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:49.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:49.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:49.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:49.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:49.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.094][private$selectFields]
biodb.TRACE[2025-03-20 05:09:49.095][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:49.096][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:49.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.101][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.111][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.112][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.113][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.115][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.119][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:49.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.138][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 05:09:49.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:49.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:49.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:49.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:49.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:49.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:49.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.167][private$selectFields]
biodb.TRACE[2025-03-20 05:09:49.169][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:49.170][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:49.171][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.174][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.185][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.187][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.192][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:49.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.211][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 05:09:49.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:49.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:49.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:49.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:49.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.239][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.240][private$selectFields]
biodb.TRACE[2025-03-20 05:09:49.242][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 05:09:49.243][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 05:09:49.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.256][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.257][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 05:09:49.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.262][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.266][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 05:09:49.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:49.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:49.285][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 05:09:49.286][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 05:09:49.296][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 05:09:49.335][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:49.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 05:09:49.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:49.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 05:09:49.349][biodb::testThat]
biodb.INFO [2025-03-20 05:09:49.351][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-20 05:09:49.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:49.355][biodb::testThat]
biodb.DEBUG[2025-03-20 05:09:49.358][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-20 05:09:49.359][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:09:49.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-20 05:09:49.365][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:09:49.367][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:09:49.368][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:09:49.370][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:09:49.372][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:09:49.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:09:49.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:49.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:49.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:49.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:49.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:49.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:49.394][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[2025-03-20 05:09:49.396][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-20 05:09:49.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:49.402][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:49.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-20 05:09:50.181][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-20 05:09:50.953][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:50.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-20 05:09:50.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-20 05:09:50.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-20 05:09:50.972][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:09:50.975][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:09:50.977][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:09:50.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:50.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:50.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:50.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:50.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:50.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:50.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:51.002][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.017][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:51.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:51.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.025][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:51.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:51.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.031][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:51.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:51.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.041][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:51.043][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:51.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.048][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:51.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:51.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.055][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:51.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:51.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.063][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:51.065][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:51.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.070][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:51.072][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:51.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.078][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:51.079][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:51.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:51.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:51.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:51.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:51.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:51.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:51.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:51.180][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-20 05:09:51.181][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-20 05:09:51.194][biodb::testThat]
biodb.INFO [2025-03-20 05:09:51.196][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-20 05:09:51.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:51.201][biodb::testThat]
biodb.DEBUG[2025-03-20 05:09:51.218][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-20 05:09:51.220][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-20 05:09:51.221][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-20 05:09:51.224][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-20 05:09:51.226][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-20 05:09:51.227][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:09:51.229][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:09:51.230][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:09:51.232][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:09:51.234][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:09:51.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:51.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:51.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:51.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:51.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:51.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:51.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:51.255][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-20 05:09:51.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:51.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:51.263][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-20 05:09:52.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-20 05:09:53.000][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:53.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-20 05:09:53.008][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-20 05:09:53.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:53.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:53.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:53.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:53.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:53.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:53.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:53.025][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-20 05:09:53.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:53.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:53.032][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-20 05:09:53.774][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-20 05:09:54.514][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:54.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-20 05:09:54.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-20 05:09:54.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:54.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:54.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:54.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:54.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:54.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:54.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:54.541][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-20 05:09:54.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:54.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:54.549][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-20 05:09:55.292][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-20 05:09:56.030][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:56.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-20 05:09:56.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-20 05:09:56.042][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-20 05:09:56.044][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:09:56.046][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-20 05:09:56.048][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-20 05:09:56.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:56.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:56.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:56.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:56.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:56.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:56.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:56.067][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.079][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:56.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:56.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.085][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:56.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:56.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:56.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:56.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.104][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.111][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:56.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:56.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.117][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.118][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.123][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:56.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:56.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.129][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:56.130][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:56.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.156][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:56.158][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:56.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.160][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:56.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:56.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:56.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:56.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:56.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:56.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:56.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:56.216][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.217][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.227][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:56.229][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:56.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.233][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:56.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:56.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.239][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:56.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:56.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.245][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:56.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.251][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:56.253][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:56.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:56.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.263][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.264][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.274][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.276][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.286][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:56.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:56.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:56.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.297][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.299][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.309][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:56.311][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:56.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:56.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:56.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.321][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:56.323][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:56.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.327][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:56.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.333][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:56.334][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:56.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:56.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:09:56.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:56.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:56.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:56.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:56.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:56.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:09:56.410][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.422][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:56.423][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:56.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.426][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.428][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:09:56.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:09:56.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.441][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:56.442][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:56.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:09:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:09:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.454][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:56.456][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:56.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:09:56.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:09:56.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.467][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:09:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.480][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.481][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:09:56.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.493][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:56.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:56.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.500][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:09:56.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:09:56.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.524][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:56.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:56.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:56.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:56.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:56.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:09:56.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:09:56.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.551][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:56.553][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:56.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:09:56.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:09:56.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:09:56.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:09:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:09:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:09:56.665][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-20 05:09:56.666][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-20 05:09:56.668][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-20 05:09:56.704][biodb::testThat]
biodb.INFO [2025-03-20 05:09:56.706][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-20 05:09:56.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:56.709][biodb::testThat]
biodb.INFO [2025-03-20 05:09:56.745][biodb::testThat]
biodb.INFO [2025-03-20 05:09:56.747][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-20 05:09:56.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:56.749][biodb::testThat]
biodb.INFO [2025-03-20 05:09:56.761][biodb::testThat]
biodb.INFO [2025-03-20 05:09:56.762][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-20 05:09:56.764][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:56.765][biodb::testThat]
biodb.DEBUG[2025-03-20 05:09:56.769][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[2025-03-20 05:09:56.774][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:56.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:56.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:09:57.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:09:58.651][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:09:58.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-20 05:09:58.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-20 05:09:58.676][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:09:58.678][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:09:58.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:58.681][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:09:58.682][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:58.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:09:58.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:09:58.687][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 05:09:58.689][biodb::testThat]
biodb.INFO [2025-03-20 05:09:58.690][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-20 05:09:58.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:58.693][biodb::testThat]
biodb.ERROR[2025-03-20 05:09:58.713][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-20 05:09:58.741][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-20 05:09:58.761][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 05:09:58.763][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 05:09:58.765][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 05:09:58.766][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 05:09:58.767][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:58.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:58.770][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:58.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:58.773][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 05:09:58.790][biodb::testContext]
biodb.INFO [2025-03-20 05:09:58.792][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:09:58.793][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-20 05:09:58.795][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:09:58.796][biodb::testContext]
biodb.INFO [2025-03-20 05:09:58.799][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:09:58.802][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 05:09:58.807][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:09:58.809][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 05:09:58.810][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.815][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[2025-03-20 05:09:58.816][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 05:09:58.818][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.838][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 05:09:58.840][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.846][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 05:09:58.848][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 05:09:58.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 05:09:58.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.856][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 05:09:58.857][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 05:09:58.859][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.865][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 05:09:58.867][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 05:09:58.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.872][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 05:09:58.874][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 05:09:58.876][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 05:09:58.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.881][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 05:09:58.883][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.888][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 05:09:58.890][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 05:09:58.891][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 05:09:58.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.895][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[2025-03-20 05:09:58.896][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:09:58.898][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 05:09:58.899][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 05:09:58.901][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 05:09:58.902][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 05:09:58.904][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 05:09:58.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.909][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 05:09:58.911][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 05:09:58.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.916][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 05:09:58.917][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 05:09:58.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.923][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 05:09:58.924][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 05:09:58.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.929][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 05:09:58.931][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 05:09:58.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.936][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 05:09:58.938][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 05:09:58.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.943][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:09:58.945][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 05:09:58.949][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 05:09:58.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.955][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 05:09:58.956][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 05:09:58.957][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 05:09:58.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:58.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:58.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:58.963][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 05:09:58.966][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:58.967][self$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[2025-03-20 05:09:58.969][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:58.970][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:09:58.971][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:58.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:09:58.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:58.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:09:58.977][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:09:58.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:09:58.980][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:58.981][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 05:09:58.983][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:09:58.984][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:58.986][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:58.987][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:09:58.987][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:09:58.987][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:09:58.987][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:09:58.987][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:09:58.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:09:58.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:58.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:58.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:09:58.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:58.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:58.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:09:58.998][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:58.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:09:59.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:09:59.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.003][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.005][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 05:09:59.008][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:09:59.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:09:59.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:09:59.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:09:59.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.024][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 05:09:59.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:09:59.026][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.029][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:09:59.029][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:09:59.029][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:09:59.029][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:09:59.029][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:09:59.031][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:09:59.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:09:59.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.041][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.042][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:09:59.043][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:09:59.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.046][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.048][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 05:09:59.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.052][self$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[2025-03-20 05:09:59.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:09:59.056][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.057][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.059][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.062][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:09:59.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:09:59.065][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.066][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 05:09:59.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:09:59.069][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.072][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.073][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:09:59.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:09:59.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.082][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.091][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:09:59.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:09:59.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.098][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.099][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 05:09:59.102][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.103][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:09:59.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:09:59.107][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.109][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.112][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.113][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:09:59.114][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:09:59.116][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.117][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 05:09:59.119][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:09:59.120][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.121][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.123][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.124][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:09:59.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.128][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:09:59.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.134][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:09:59.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:09:59.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.139][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:09:59.141][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:09:59.142][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.156][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[2025-03-20 05:09:59.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.187][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[2025-03-20 05:09:59.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.224][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[2025-03-20 05:09:59.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.243][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[2025-03-20 05:09:59.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.251][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 05:09:59.253][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 05:09:59.255][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 05:09:59.257][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 05:09:59.259][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:09:59.261][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 05:09:59.263][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 05:09:59.265][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 05:09:59.267][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 05:09:59.270][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 05:09:59.272][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:09:59.274][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 05:09:59.276][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 05:09:59.278][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 05:09:59.280][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 05:09:59.282][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 05:09:59.284][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 05:09:59.286][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 05:09:59.288][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:09:59.290][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 05:09:59.292][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 05:09:59.294][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 05:09:59.296][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 05:09:59.298][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 05:09:59.300][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 05:09:59.302][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 05:09:59.304][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 05:09:59.306][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 05:09:59.309][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 05:09:59.310][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 05:09:59.313][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 05:09:59.315][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 05:09:59.317][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 05:09:59.319][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 05:09:59.321][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 05:09:59.548][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 05:09:59.551][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 05:09:59.552][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 05:09:59.554][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 05:09:59.556][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 05:09:59.558][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 05:09:59.560][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 05:09:59.562][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 05:09:59.564][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 05:09:59.566][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 05:09:59.568][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 05:09:59.570][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 05:09:59.572][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 05:09:59.574][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 05:09:59.576][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 05:09:59.578][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 05:09:59.580][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 05:09:59.582][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 05:09:59.584][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 05:09:59.586][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 05:09:59.588][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 05:09:59.590][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 05:09:59.592][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 05:09:59.594][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 05:09:59.596][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 05:09:59.598][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 05:09:59.600][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 05:09:59.602][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 05:09:59.603][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 05:09:59.605][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 05:09:59.607][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 05:09:59.609][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:09:59.611][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:09:59.613][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 05:09:59.615][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 05:09:59.617][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 05:09:59.619][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 05:09:59.621][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 05:09:59.623][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 05:09:59.625][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 05:09:59.627][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 05:09:59.629][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 05:09:59.631][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 05:09:59.633][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 05:09:59.635][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 05:09:59.637][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 05:09:59.639][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 05:09:59.641][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 05:09:59.643][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 05:09:59.646][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:09:59.647][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:09:59.648][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.651][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.652][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[2025-03-20 05:09:59.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.731][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[2025-03-20 05:09:59.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.748][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[2025-03-20 05:09:59.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.783][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.DEBUG[2025-03-20 05:09:59.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:09:59.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:09:59.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:09:59.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:09:59.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:09:59.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:09:59.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:09:59.811][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 05:09:59.813][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 05:09:59.816][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.818][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.819][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:09:59.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.825][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.826][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 05:09:59.827][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 05:09:59.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:09:59.830][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.831][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 05:09:59.833][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 05:09:59.834][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 05:09:59.836][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 05:09:59.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:09:59.837][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:09:59.837][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:09:59.839][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 05:09:59.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:09:59.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:09:59.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:09:59.847][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:09:59.848][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:09:59.848][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 05:09:59.849][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:09:59.851][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:09:59.852][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 05:09:59.853][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 05:09:59.853][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 05:09:59.855][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:09:59.857][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:09:59.860][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 05:09:59.862][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:09:59.864][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:09:59.866][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:09:59.871][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 05:09:59.872][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 05:09:59.874][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 05:09:59.876][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 05:09:59.877][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:09:59.879][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:09:59.881][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 05:09:59.882][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 05:09:59.884][biodb::testThat]
biodb.INFO [2025-03-20 05:09:59.885][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-20 05:09:59.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:09:59.888][biodb::testThat]
biodb.DEBUG[2025-03-20 05:09:59.893][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 05:09:59.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:09:59.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:09:59.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-20 05:10:01.679][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-20 05:10:02.656][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:02.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-20 05:10:02.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-20 05:10:02.672][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[2025-03-20 05:10:02.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:02.679][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:02.681][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:10:04.189][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:10:05.142][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:05.145][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-20 05:10:05.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-20 05:10:05.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:05.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:05.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:05.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:05.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:05.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:05.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:05.198][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:10:05.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:05.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:05.207][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:10:06.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:10:06.747][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:06.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-20 05:10:06.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-20 05:10:06.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.774][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[2025-03-20 05:10:06.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:06.848][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[2025-03-20 05:10:06.853][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:06.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 05:10:06.857][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:06.859][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 05:10:06.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.876][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.DEBUG[2025-03-20 05:10:06.879][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[2025-03-20 05:10:06.884][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:06.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 05:10:06.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:06.890][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 05:10:06.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.906][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[2025-03-20 05:10:06.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:06.929][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[2025-03-20 05:10:06.934][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:06.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 05:10:06.938][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:06.940][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 05:10:06.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.956][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[2025-03-20 05:10:06.958][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[2025-03-20 05:10:06.963][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:06.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 05:10:06.966][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:06.968][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 05:10:06.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:06.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:06.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:06.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:06.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:06.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:06.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:06.986][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[2025-03-20 05:10:06.991][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:06.992][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:06.995][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:10:07.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:10:08.511][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:08.515][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-20 05:10:08.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-20 05:10:08.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:08.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:08.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:08.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:08.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:08.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:08.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 05:10:08.553][biodb::testThat]
biodb.INFO [2025-03-20 05:10:08.555][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-20 05:10:08.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:10:08.558][biodb::testThat]
biodb.DEBUG[2025-03-20 05:10:08.564][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:10:08.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:08.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:08.574][private$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[2025-03-20 05:10:09.615][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[2025-03-20 05:10:10.355][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:10.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-20 05:10:10.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-20 05:10:10.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:10.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:10.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:10.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:10.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:10.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:10.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:10.388][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[2025-03-20 05:10:10.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:10.418][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:10.421][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 05:10:11.144][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 05:10:11.866][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:11.870][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-20 05:10:11.876][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-20 05:10:11.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:11.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:11.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:11.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:11.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:11.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 05:10:11.900][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 05:10:11.902][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 05:10:11.903][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 05:10:11.905][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 05:10:11.906][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:11.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:11.908][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:11.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:11.911][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 05:10:11.918][biodb::testContext]
biodb.INFO [2025-03-20 05:10:11.920][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:10:11.921][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-20 05:10:11.922][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:10:11.924][biodb::testContext]
biodb.INFO [2025-03-20 05:10:11.927][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:10:11.929][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 05:10:11.934][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:11.936][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 05:10:11.937][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.943][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 05:10:11.944][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.949][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 05:10:11.951][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.956][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 05:10:11.957][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 05:10:11.959][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 05:10:11.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.964][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 05:10:11.966][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 05:10:11.967][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.973][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 05:10:11.975][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 05:10:11.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.980][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 05:10:11.981][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 05:10:11.983][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 05:10:11.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.988][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 05:10:11.989][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:11.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:11.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:11.995][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 05:10:11.996][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 05:10:11.997][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 05:10:11.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.003][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:10:12.004][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 05:10:12.006][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 05:10:12.007][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 05:10:12.008][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 05:10:12.010][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 05:10:12.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.015][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 05:10:12.017][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 05:10:12.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.022][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 05:10:12.023][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 05:10:12.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.028][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 05:10:12.030][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 05:10:12.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.034][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 05:10:12.036][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 05:10:12.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.041][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 05:10:12.042][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 05:10:12.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.046][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.DEBUG[2025-03-20 05:10:12.048][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:10:12.049][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 05:10:12.054][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 05:10:12.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.059][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 05:10:12.061][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 05:10:12.062][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 05:10:12.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.066][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[2025-03-20 05:10:12.067][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 05:10:12.070][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.071][self$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[2025-03-20 05:10:12.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.074][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:12.075][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.077][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.078][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.079][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.081][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:10:12.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:12.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.085][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 05:10:12.086][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:12.088][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.089][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.090][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:12.090][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:12.090][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:12.090][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:10:12.090][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:10:12.092][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:12.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.095][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:12.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.101][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:12.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:12.104][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.106][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.119][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 05:10:12.123][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.124][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:10:12.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:12.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.131][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.134][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:10:12.135][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:12.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.138][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 05:10:12.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:12.141][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.142][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.144][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:12.144][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:12.144][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:12.144][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:10:12.144][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:10:12.145][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:12.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:12.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.153][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.154][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:12.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:12.158][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.159][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.161][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 05:10:12.163][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.165][self$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[2025-03-20 05:10:12.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:12.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:10:12.175][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:12.177][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.178][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 05:10:12.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:12.181][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.183][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.185][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:12.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:12.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.194][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:12.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:12.197][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.199][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.200][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 05:10:12.203][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.204][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:10:12.205][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.207][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:12.208][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.211][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.212][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.213][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:10:12.215][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:12.216][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.218][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 05:10:12.219][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:12.221][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.222][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.224][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.225][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:12.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:12.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.234][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.235][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:12.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:12.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.241][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:12.243][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:12.244][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.302][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.DEBUG[2025-03-20 05:10:12.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.321][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[2025-03-20 05:10:12.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.354][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 05:10:12.363][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 05:10:12.365][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 05:10:12.367][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 05:10:12.369][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:10:12.372][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 05:10:12.374][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 05:10:12.376][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 05:10:12.378][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 05:10:12.380][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 05:10:12.382][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:10:12.384][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 05:10:12.386][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 05:10:12.388][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 05:10:12.390][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 05:10:12.392][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 05:10:12.395][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 05:10:12.397][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 05:10:12.399][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:10:12.401][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 05:10:12.403][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 05:10:12.405][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 05:10:12.407][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 05:10:12.409][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 05:10:12.411][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 05:10:12.413][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 05:10:12.416][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 05:10:12.418][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 05:10:12.420][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 05:10:12.422][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 05:10:12.424][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 05:10:12.426][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 05:10:12.428][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 05:10:12.430][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 05:10:12.432][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 05:10:12.434][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 05:10:12.436][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 05:10:12.438][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 05:10:12.440][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 05:10:12.443][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 05:10:12.445][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 05:10:12.447][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 05:10:12.449][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 05:10:12.451][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 05:10:12.453][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 05:10:12.455][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 05:10:12.457][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 05:10:12.459][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 05:10:12.461][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 05:10:12.463][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 05:10:12.466][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 05:10:12.468][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 05:10:12.470][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 05:10:12.472][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 05:10:12.474][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 05:10:12.476][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 05:10:12.478][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 05:10:12.480][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 05:10:12.482][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 05:10:12.484][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 05:10:12.486][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 05:10:12.488][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 05:10:12.490][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 05:10:12.492][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 05:10:12.494][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 05:10:12.496][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 05:10:12.498][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:10:12.500][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:10:12.502][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 05:10:12.504][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 05:10:12.506][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 05:10:12.509][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 05:10:12.511][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 05:10:12.513][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 05:10:12.515][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 05:10:12.517][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 05:10:12.519][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 05:10:12.521][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 05:10:12.523][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 05:10:12.525][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 05:10:12.527][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 05:10:12.529][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 05:10:12.531][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 05:10:12.533][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 05:10:12.536][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:10:12.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:12.538][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.541][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.542][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[2025-03-20 05:10:12.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.568][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[2025-03-20 05:10:12.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.586][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[2025-03-20 05:10:12.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.595][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[2025-03-20 05:10:12.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.630][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[2025-03-20 05:10:12.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.664][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.DEBUG[2025-03-20 05:10:12.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.672][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[2025-03-20 05:10:12.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.702][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[2025-03-20 05:10:12.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:12.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:12.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:12.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:12.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:12.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:12.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:12.715][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 05:10:12.717][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 05:10:12.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.723][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.724][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:12.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.731][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.732][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 05:10:12.734][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 05:10:12.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:12.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.739][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 05:10:12.741][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 05:10:12.742][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 05:10:12.744][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:12.746][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:12.746][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:12.746][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:12.748][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 05:10:12.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.752][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:12.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:12.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:12.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:12.759][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:10:12.759][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 05:10:12.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:12.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:12.764][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:12.765][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 05:10:12.765][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 05:10:12.768][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:10:12.771][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:10:12.773][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 05:10:12.776][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:10:12.779][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:10:12.781][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:10:12.787][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 05:10:12.789][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 05:10:12.792][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 05:10:12.795][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 05:10:12.797][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:10:12.799][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:10:12.801][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 05:10:12.803][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 05:10:12.805][biodb::testThat]
biodb.INFO [2025-03-20 05:10:12.807][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-20 05:10:12.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:10:12.810][biodb::testThat]
biodb.DEBUG[2025-03-20 05:10:12.816][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 05:10:12.823][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:12.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 05:10:12.828][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:12.831][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 05:10:12.837][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 05:10:12.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:12.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:12.848][private$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[2025-03-20 05:10:13.639][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[2025-03-20 05:10:14.577][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:14.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-20 05:10:14.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-20 05:10:14.604][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 05:10:14.606][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 05:10:14.608][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 05:10:14.610][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 05:10:14.612][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:14.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:14.615][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:14.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:14.618][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.620][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.INFO [2025-03-20 05:10:14.627][biodb::testContext]
biodb.INFO [2025-03-20 05:10:14.629][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:10:14.631][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-20 05:10:14.633][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 05:10:14.635][biodb::testContext]
biodb.INFO [2025-03-20 05:10:14.669][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:10:14.678][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 05:10:14.684][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:14.686][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 05:10:14.688][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.695][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 05:10:14.697][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.702][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[2025-03-20 05:10:14.704][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 05:10:14.706][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.713][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 05:10:14.715][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 05:10:14.717][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 05:10:14.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.723][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[2025-03-20 05:10:14.725][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 05:10:14.727][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 05:10:14.729][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.736][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 05:10:14.738][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 05:10:14.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.745][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 05:10:14.747][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 05:10:14.749][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 05:10:14.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.756][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 05:10:14.758][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.765][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 05:10:14.767][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 05:10:14.769][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 05:10:14.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.776][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:10:14.778][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 05:10:14.779][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 05:10:14.781][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 05:10:14.782][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 05:10:14.784][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 05:10:14.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.790][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 05:10:14.792][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 05:10:14.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.797][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 05:10:14.799][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 05:10:14.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.804][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 05:10:14.806][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 05:10:14.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.812][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 05:10:14.813][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 05:10:14.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.819][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 05:10:14.820][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 05:10:14.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.826][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 05:10:14.828][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 05:10:14.833][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 05:10:14.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.839][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 05:10:14.840][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 05:10:14.842][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 05:10:14.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:14.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:14.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:14.848][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 05:10:14.850][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.852][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 05:10:14.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.856][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:14.857][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.861][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.862][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.864][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:10:14.866][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:14.868][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.869][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 05:10:14.871][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:14.873][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.875][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:14.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:14.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:14.876][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:10:14.876][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:10:14.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:14.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:14.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.890][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.891][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:14.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:14.895][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.897][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.899][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 05:10:14.902][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.903][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:10:14.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.907][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:14.909][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.911][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.913][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.914][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.916][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:10:14.918][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:14.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.922][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 05:10:14.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:14.924][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.926][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.927][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:14.927][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:14.927][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:14.927][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 05:10:14.927][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 05:10:14.929][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:14.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.933][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:14.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.938][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.940][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:14.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:14.942][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.944][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.946][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 05:10:14.948][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.950][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 05:10:14.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:14.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.957][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.960][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 05:10:14.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:14.963][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.972][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 05:10:14.974][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:14.975][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.977][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:14.978][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.979][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:14.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.983][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:14.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:14.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:14.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:14.989][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:14.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:14.993][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:14.994][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:14.996][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 05:10:14.998][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.000][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 05:10:15.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:15.004][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.005][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.006][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:15.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 05:10:15.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:15.012][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:15.013][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 05:10:15.015][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:15.016][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:15.017][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.019][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:15.020][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 05:10:15.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:15.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:15.024][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:15.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:15.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:15.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.029][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:15.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:15.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:15.033][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:15.035][self$setPropertyValue]
biodb.DEBUG[2025-03-20 05:10:15.037][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:15.038][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.046][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.DEBUG[2025-03-20 05:10:15.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.065][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[2025-03-20 05:10:15.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.096][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[2025-03-20 05:10:15.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.109][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[2025-03-20 05:10:15.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.146][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[2025-03-20 05:10:15.147][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 05:10:15.149][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 05:10:15.151][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 05:10:15.154][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 05:10:15.156][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:10:15.158][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 05:10:15.160][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 05:10:15.162][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 05:10:15.164][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 05:10:15.166][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 05:10:15.168][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:10:15.170][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 05:10:15.172][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 05:10:15.174][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 05:10:15.176][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 05:10:15.178][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 05:10:15.180][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 05:10:15.182][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 05:10:15.184][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:10:15.186][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 05:10:15.188][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 05:10:15.191][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 05:10:15.193][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 05:10:15.195][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 05:10:15.197][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 05:10:15.199][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 05:10:15.201][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 05:10:15.203][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 05:10:15.213][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 05:10:15.215][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 05:10:15.218][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 05:10:15.220][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 05:10:15.222][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 05:10:15.224][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 05:10:15.226][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 05:10:15.228][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 05:10:15.230][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 05:10:15.232][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 05:10:15.234][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 05:10:15.236][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 05:10:15.238][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 05:10:15.240][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 05:10:15.242][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 05:10:15.244][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 05:10:15.246][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 05:10:15.248][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 05:10:15.250][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 05:10:15.252][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 05:10:15.254][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 05:10:15.256][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 05:10:15.258][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 05:10:15.260][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 05:10:15.262][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 05:10:15.264][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 05:10:15.266][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 05:10:15.269][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 05:10:15.271][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 05:10:15.272][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 05:10:15.275][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 05:10:15.277][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 05:10:15.278][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 05:10:15.280][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 05:10:15.282][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 05:10:15.285][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 05:10:15.287][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 05:10:15.289][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 05:10:15.291][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:10:15.293][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:10:15.295][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 05:10:15.297][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 05:10:15.299][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 05:10:15.301][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 05:10:15.303][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 05:10:15.306][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 05:10:15.308][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 05:10:15.310][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 05:10:15.312][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 05:10:15.314][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 05:10:15.316][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 05:10:15.318][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 05:10:15.320][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 05:10:15.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 05:10:15.324][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 05:10:15.327][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 05:10:15.329][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 05:10:15.330][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 05:10:15.331][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.334][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.396][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[2025-03-20 05:10:15.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.405][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[2025-03-20 05:10:15.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.440][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[2025-03-20 05:10:15.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.467][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[2025-03-20 05:10:15.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.475][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[2025-03-20 05:10:15.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 05:10:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.510][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 05:10:15.513][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 05:10:15.517][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:15.519][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.521][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.522][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 05:10:15.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.526][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.527][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.529][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 05:10:15.531][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 05:10:15.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 05:10:15.534][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.536][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 05:10:15.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 05:10:15.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 05:10:15.541][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 05:10:15.543][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 05:10:15.543][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 05:10:15.543][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 05:10:15.545][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 05:10:15.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:15.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:15.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 05:10:15.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 05:10:15.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 05:10:15.554][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 05:10:15.556][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:10:15.556][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 05:10:15.558][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 05:10:15.559][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 05:10:15.561][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 05:10:15.563][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 05:10:15.563][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 05:10:15.565][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 05:10:15.568][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 05:10:15.571][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 05:10:15.573][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 05:10:15.576][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 05:10:15.579][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 05:10:15.585][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 05:10:15.587][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 05:10:15.589][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 05:10:15.592][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 05:10:15.594][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:10:15.596][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 05:10:15.598][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 05:10:15.600][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 05:10:15.603][biodb::testThat]
biodb.INFO [2025-03-20 05:10:15.605][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-20 05:10:15.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 05:10:15.608][biodb::testThat]
biodb.DEBUG[2025-03-20 05:10:15.613][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 05:10:15.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:15.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 05:10:15.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:15.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 05:10:15.630][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[2025-03-20 05:10:15.635][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 05:10:15.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-20 05:10:15.639][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 05:10:15.641][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-20 05:10:15.649][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-20 05:10:15.651][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 05:10:15.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-20 05:10:15.655][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 05:10:15.657][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 05:10:15.658][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 05:10:15.660][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 05:10:15.661][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 05:10:15.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 05:10:15.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:15.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:15.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:15.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:15.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:15.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:15.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 05:10:15.683][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-20 05:10:15.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 05:10:15.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 05:10:15.691][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-20 05:10:20.008][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-20 05:10:21.349][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 05:10:21.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-20 05:10:21.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-20 05:10:21.366][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-20 05:10:21.369][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 05:10:21.372][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 05:10:21.374][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 05:10:21.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 05:10:21.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:21.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:21.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:21.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:21.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:21.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 05:10:21.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.414][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:10:21.416][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:10:21.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.439][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 05:10:21.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 05:10:21.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.445][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:10:21.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:10:21.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.450][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 05:10:21.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 05:10:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.458][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 05:10:21.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 05:10:21.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.465][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 05:10:21.467][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 05:10:21.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.472][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:10:21.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:10:21.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.479][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:10:21.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 05:10:21.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.485][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:10:21.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:10:21.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.492][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 05:10:21.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 05:10:21.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.498][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:10:21.500][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:10:21.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:10:21.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 05:10:21.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.511][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:10:21.513][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:10:21.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 05:10:21.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 05:10:21.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.524][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:10:21.526][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:10:21.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.531][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 05:10:21.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 05:10:21.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:10:21.539][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:10:21.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.544][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 05:10:21.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 05:10:21.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 05:10:21.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 05:10:21.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 05:10:21.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 05:10:21.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 05:10:21.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 05:10:21.607][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-20 05:10:21.612][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 05:10:21.614][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 05:10:21.615][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 05:10:21.616][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 05:10:21.618][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 05:10:21.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 05:10:21.620][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 05:10:21.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 05:10:21.622][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 05:10:21.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
28.478 45.749 441.510
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.166 | 0.044 | 5.484 | |
| ChebiEntry | 0.241 | 0.006 | 0.248 | |